Multi-reflecting time-of-flight mass spectrometer and method of use

ABSTRACT

A multiple reflecting time-of-flight mass spectrometer (MR-TOF MS) and method of analysis are disclosed. The flight path of ions is folded along a trajectory by electrostatic mirrors. The longer flight path provides higher resolution while maintaining a moderate instrument size.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention generally relates to the area of mass spectroscopicanalysis, and in particular to a multi reflecting time-of-flight massspectrometer (MR-TOF MS) and a method of use.

2. State of the Art

Mass spectrometry is a well recognized tool of analytical chemistry,used for identification and quantitative analysis of various compoundsand mixtures. The sensitivity and resolution of such analysis is animportant concern for practical use. It has been well recognized thatresolution of TOF MS is proportional to the length of the flight path.However, it is recognized it is difficult to increase the flight pathwhile keeping the instrument to a reasonable size. A proposed solutionis multi-reflecting time-of-flight mass spectrometers (M-TOF MS). Theuse of MR-TOF MS became possible after the introduction of anelectrostatic ion mirror with time-of-flight focusing properties. U.S.Pat. No. 4,072,862, Soviet Patent No. SU198034 and Sov. J. Tech. Phys.41 (1971) 1498 disclose an ion mirror to improve the focusing of ionenergy in time-of-flight instruments. The use of the ion mirrorautomatically causes a single folding of ion flight path.

H. Wollnik realized a potential of ion mirrors for implementing amulti-reflecting MR-TOF MS. United Kingdom Patent No. GB2080021 suggestsa way of reducing the full length of an instrument by folding the ionpath between multiple gridless mirrors. Two rows of such mirrors may bealigned in the same plane or located on two opposite parallel circles(FIG. 1). Introduction of gridless ion mirrors with spatial ion focusingwas intended to reduce ion losses and keep the ion beam confinedregardless of the number of reflections (more details in U.S. Pat. No.5,017,780). The gridless mirrors disclosed in GB 2080021 were to provideindependence of ion flight time from the ion energy. Two types of MR-TOFMS are disclosed: (a) folded path’ scheme, which is equivalent tocombining N sequential reflecting TOF MS, and where the flight path isfolded along a jig-saw trajectory; and (b) ‘coaxial reflecting’ scheme,which employs multiple ion reflections between two axially aligned ionmirrors using pulsed ion admission and release. The ‘coaxial reflecting’scheme was also described by H. Wollnik et al. in Mass Spec. Rev., 1993,12, p.109 and was implemented in the work published in the Int. J. MassSpectrom. Ion Proc. 227 (2003) 217. Resolution of 50,000 was achievedafter 50 turns in a moderate size (30 cm) TOF MS. Gridless and spatiallyfocusing ion mirrors indeed preserved ions of interest (losses werebelow factor of 2), though the admitted mass range shrank proportionallywith the number of cycles.

Another type, cyclic MR-TOF MS was described in papers by H. Wollnik,Nucl. Instr. Meth., A258 (1987) 289, and Sakurai et al, Nucl. Instr.Meth., A427 (1999) 182. Ions are kept in closed orbits usingelectrostatic or magnetic deflectors. The scheme employed multiplerepetitive cycles, which shrank mass range, similarly to the coaxialreflecting scheme.

A folded path MR-TOF MS using two-dimensional gridless mirrors wasdisclosed in Soviet Union Patent SU1725289. The MR-TOF MS comprised twoidentical mirrors, built of bars, were parallel and symmetric withrespect to the median plane between the mirrors and also to the plane ofthe folded ion path (FIG. 2). Mirror geometry and potentials werearranged to focus the ion beam spatially across the plane of the foldedion path and provide second-order time of flight focusing with respectto the ion energy. The ions experienced multiple reflections between theplanar mirrors, while slowly drifting towards the detector in aso-called shift direction (here X-axis). The number of cycles andresolution were adjusted by varying the ion injection angle.

Nazarenko's prototype of a ‘folded path’ MR-TOF MS with planar gridlessmirrors, having spatial and time-of-flight focusing properties did notprovide ion focusing in the shift direction, thus limiting the number ofreflection cycles. Besides, the ion mirrors used in the prototype didnot provide time-of-flight focusing with respect to spatial ion spreadacross the plane of the folded ion path, so that a use of diverging orwide beams would in fact ruin the time-of-flight resolution and wouldmake an extension of flight path pointless. In other words, the schemefailed to deliver an acceptable analyzer and thus the ability of workingwith real ion sources. Lastly, the Nazarenko prototype has noimplication on the type of ion source, nor on efficient ways of couplingbetween MR-TOF MS and various ion sources,

The type of ion source, its spatial and timing characteristics of ionbeam, as well as geometrical constrains are the important considerationsin the design of MR-TOF MS. Compatibility with single reflecting TOF MSdoes not automatically mean that a source is well suited for MR-TOF MS.For example, pulsed ion sources, like secondary ion SIMS ormatrix-assisted desorption/ionization MALDI, are very compatible withTOF MS and such instruments are characterized by high resolution andmoderate ion losses caused by spatial ion divergence. Switching toMR-TOF MS introduces new problems. On one hand, a pulsed nature of suchsources suits well an extension of flight time in MR-TOF MS sincefrequency of ionizing pulses is adjustable. On the other hand,instability of MALDI ions is a limiting factor on flight time extension.

Gaseous ion sources, like electrospray (ESI), atmospheric pressurechemical ionization (APCI) atmospheric pressure photo-ionization (APPI),electron impact (EI), chemical ionization (CI), photo-ionization (CI) orinductively-coupled plasma (ICP) are known to produce stable ions, butthey generate intrinsically continuous ion beams, or quasi-continuousion beams, as in case of recently introduced gas filled MALDI ion sourcedescribed in U.S. Pat. Nos. 6,331,702, and 6,504,150. TOF MS has beensuccessfully coupled with continuous, and later to quasi-continuous ionsources, after introduction of an orthogonal ion acceleration scheme(o-TOF MS) (see U.S. Pat. No. 5,070,240, WO9103071, Soviet patentSU1681340), efficiently converting continuous ion beams into ion pulsedpackets. Gaseous ion sources in combination with a collisional-coolingion guide (U.S. Pat. No. 4,963,736) produce cold ion beams with lowvelocity spread along the axis of TOF MS, which help to achieve high TOFresolution in excess of 10,000. However, using MR-TOF MS would reducethe duty cycle of orthogonal acceleration and thus drop sensitivity.

U.S. Pat. No. 6,107,625 suggests that a further increase of resolutionof o-TOF MS is mostly limited by a so-called ‘turn-around time’ andincreasing of flight path improves resolution. The '625 patent suggestsa coupling of external ESI source to a ‘coaxial reflecting’ MR-TOF MSvia an orthogonal accelerator, combined with an ion mirror and multipledeflectors, such as shown in FIG. 3. To improve the sampling of thecontinuous ion beam, the interface employs a linear ion trap, storingions between rare ion pulses. Melvin Park et. al. in the articleentitled ‘Analytical Figure of Merits of a Multi-Pass Time-of-FlightMass Spectrometer’, extended abstract on ASMS 2001, www.asms.org, MR-TOFMS demonstrated resolution of 60,000 using 6 cycles of reflections in ac.a. 1 m long instrument. However, the use of ion mirrors with gridscaused severe ion scattering and ion losses. Coaxial reflecting MR-TOFMS improved resolution but shrank mass range proportionally.

ESI with orthogonal injection has been also coupled to an MR-TOF MS witha folded ion path (see EP 1 237 044 A2 and J. Hoyes et al. in extendedabstract ASMS 2000 ‘A high resolution Orthogonal TOF with selectabledrift length’ www.asms.org). The invention allows converting an existingcommercial o-TOF into a dual reflecting instrument by introducing anadditional short reflector between orthogonal source and detector.Energy of continuous ion beam controls number of ion reflections. The‘folded path’ MR-TOF MS retains full mass range and considerablyimproves resolution, but it also reduces duty cycle and geometricalefficiency of ion sampling into the orthogonal accelerator in additionto ion losses and scattering occurring at every pass through meshes inboth ion mirrors.

The two above examples demonstrate that a conventional orthogonalacceleration becomes inefficient in MR-TOF MS, particularly at extendedflight times. There have been multiple attempts of improving pulsed ionsampling from continuous ion beams, mostly employing ion storage inradio-frequency (RF) traps, like 3-D ion trap (IT) in the paper of B. M.Chien et al. ‘The design and performance of an ion trapstorage-reflectron time-of-flight mass spectrometer’ InternationalJournal of Mass Spectrometry and Ion Processes 131 (1994) 149-119,linear ion trap (LIT) in U.S. Pat. No. 5,763,878, U.S. Pat. No.5,847,386 (FIGS. 29-31), U.S. Pat. No. 6,111,250 (FIGS. 29-31), U.S.Pat. No. 6,545,268 and WO9930350 or dual LIT (GB2378312) and ring iontrap in paper of A. Luca et al., ‘On the combination of a linear fieldfree trap with a time-of-flight mass spectrometer’, Rev. Sci. Instrum.V.72, #7 (2001), p 2900-2908. Since all of those solutions compromisetemporal and/or spatial spread of ejected ion packets, the orthogonalinjection is still the method of choice for singly reflecting TOF MS.Some trapping features are used in an intermediate scheme in U.S. Pat.No. 6,020,586, combining both an ion trapping step and an orthogonalacceleration. Slow ion packets are periodically ejected out of storingion guide into a synchronized orthogonal accelerator. Compared toconventional o-TOF MS the scheme improves sensitivity, while moderatelysacrificing resolution and mass range. The scheme has been coupled tocoaxial MR-TOF MS in already described reference by M. Park. However,such instrument does not provide full mass range. It is still desirableto improve conversion of continuous ion beam into ion pulses fullysuitable for TOF MS and particularly to multi-reflecting TOF MS.

Multiple reflecting TOF is also employed in tandem mass spectrometer ina co-pending application of one of the author (WO2004008481). A slowMR-TOF MS is used for slow separation of parent ions at a millisecondtime scale and a short orthogonal TOF is used for fast mass analysis offragments at a microsecond time scale. Fast collisional cell is usedin-between to fragment ions without smearing time-of-flight separationin the MR-TOF MS. The scheme delivers a novel quality: it allowsparallel or ‘multi-dimensional’ MS-MS analysis, where fragment spectraare simultaneously acquired for multiple parents without mixing them.The scheme has a drawback that parent ions spread in the shift directionwhich strongly limits acceptance of analyzer and requires smallerdivergence of ion beam coming out of the ion source. A higher acceptanceof MR-TOF MS is desirable.

Summarizing the above, the MR-TOF MS of the prior art do not havespatial and time of-flight focusing to provide a certain retaining ofion beam along a substantially extended flight path. Most of referencesdescribe MR-TOF analyzer without considering their compatibility withion sources as well as their utility in tandem mass spectrometers. Infact, a limited acceptance of the known MR-TOF analyzers seriouslylimits such coupling and is expected to cause ion losses atsubstantially elongated flight paths. Some references are made to actualcoupling of MR-TOF MS to continuous ion sources, demonstrating strongimprovement of resolution. However, resolution is gained at the expenseof losing sensitivity and, in the case of coaxial reflections, ofshrinking mass range. Therefore, there is a need for TOF massspectrometer working with intrinsically continuous or quasi-continuousion sources, and superior to o-TOF by a set of major analyticalcharacteristics, namely—sensitivity, mass range and resolution. There isalso a need for better schemes of coupling TOF MS into tandem massspectrometers.

SUMMARY OF THE INVENTION

The inventors have realized that acceptance and resolution of MR-TOF MSwith two-dimensional planar mirrors could be substantially increased by:

-   -   (A) using a periodic set of lenses in a drift space, providing        focusing in a shift direction;    -   (B) employing a geometry of planar mirrors with at least 4        electrodes, which allows not only a known spatial ion focusing        and a time-of-flight focusing with regards to energy, but also a        novel time-of-flight focusing with regards to spatial spread.

The inventors further realized that an improved acceptance of the MR-TOFMS of the invention allows its efficient coupling to continuous ionsources via an ion storage device. Continuously arriving ions could bestored and pulse ejected out of a storing device, such as ion guide, IT,LIT or a ring ion trap thus saving ions between rare pulses of MR-TOFMS, sparse compared to o-TOF MS.

The MR-TOF MS of the invention provides an advantageous combination ofion optics features, compared to prior art, since:

-   -   It has a full mass range, a property of a ‘folded path’ scheme;    -   It eliminates ion losses on meshes, since mirrors are gridless,    -   It efficiently consumes continuous ion beams by storing ions in        an ion trap with pulse ion ejection at lower frequency;    -   It accepts wide ion beam produced by such traps, since the        analyzer has a spatial focusing by periodic lens in a shift        direction and spatial focusing by mirrors across the plane of        the folded ion path;    -   It improves resolution by providing a high-order time-of-flight        focusing with respect to energy and, which is novel, to spatial        spread of ion packets;    -   It tolerates a larger turn-around time of ion packets by        extension of the flight time, using folded path in multiple        reflections of a well confined ion beam and as a result        tolerates schemes with ion storing and pulsing out of various        ion traps;    -   The longer flight time brings another advantage—slower and less        expensive detector and data acquisition system, both currently        being very costly parts of TOF mass spectrometers.

The invention introduces a completely novel to MR-TOF MSfeature—multiple lenses, optimally positioned in the middle of driftspace, preferably with a period corresponding to ion shift per integernumber of turns. Periodic lenses allow focusing of the beam and, thus,insure a stable confinement of ions along an extended folded ion path.The set of lenses brings the novel quality to MR-TOF: beam spatial andangular spreads stay limited even after an extremely large number ofreflections (actually achieved if using reflections in the shiftdirection as well). Even more, using ion optics simulation the inventorsfound out that ion motion in the novel MR-TOF efficiently withstandsvarious external distortions, like inaccuracy of geometry, strayelectric and magnetic fields of pumps and gauges, as well as spacecharge of the ion beam itself. The MR-TOF returns ions into vicinity ofmain trajectory in spite of those distortions, similar to trapping inthe potential grove. The feature of periodic lenses allows compactpackaging of MR-TOF MS with an extended flight path, combined with aconfident full transmission of ion beam.

The lens tuning allows periodic, repeatable focusing in a shiftdirection, achieved when focal length F matches an integer number ofhalf reflections or quarters of full ion turns (P/4), F=N*P/4. The mosttight focusing occurs when F=P/4. Such tight focusing is advantageousfor minimizing shift per turn and making instrument compact. It isimportant that even under the condition of such tight focusing lensesremain weak because of a relatively long ion path per turn, andtherefore they introduce only minor incorrigible time-of-flightaberrations with respect to the ion spatial spread in the plane of thefolded ion path. Planar lenses, substantially elongated across the plainof ion path, provide an advantage of fairly independent tuning ofspatial focusing by ion mirrors and by periodic lenses, since they focusin different directions. Besides, such lenses may also incorporatesteering by using asymmetric voltages on side plates.

The invention allows further increase of the flight path length byemploying reflections in a shift direction. Such reflections can beachieved, for example, by deflection plates, located on the sides ofshift path in the middle of drift space between the mirrors. Deflectionplates could operate constantly or in a pulsed mode to allow ion gating.A single reflection does not affect mass range, while a further increaseof the flight path by multiple reflections in shift direction isachieved at the expense of mass range. The deflection plates could bealso used to bypass the analyzer and to steer ions into a receiver.

Novel focusing properties of the mirrors of the invention are providedby choosing a proper distance between the mirrors and adjustment ofelectrode potentials. Such adjustment results in the 3rd-ordertime-of-flight focusing on ion energy, 2nd-order time-of-flight focusingwith respect to the spatial ion spread across the plane of the foldedion path and spatial focusing across the said plane. The inventorsrealized that elimination of high-order time-of-flight aberrations isstable with respect to assembly defects as well as to moderatevariations of the drift lengths and electrode potentials. Therefore, ahigh resolving power could be obtained by tuning of novel MR-TOF MSwhile adjusting only one electrode potential, in fact, varying oneparameter—a linear dependence of the ion flight time on the ion energy.

The previously described focusing properties are realized, for example,in planar 4-electrode mirrors, composed of thick square frames,substantially elongated in a shift direction. The desired fieldstructure also could be made using thin plates with slots, bars,cylinders, or curved electrodes. The edges of two-dimensional mirrorscould be efficiently terminated using printed circuit boards to shortenthe total physical length of the MR-TOF MS. Having more electrodes isvery likely to further improve mirror parameters, but complicates thesystem.

In a preferred mode the ion source and the ion detector are located inthe drift space between the mirrors. In such configuration the foldedion path remains far from mirror edges and the mirrors can be operatedin a static mode to achieve better stability and mass accuracy of theMR-TOF MS. However, the invention is well compatible with a pulsed ionadmission from external source or ion release through ion mirrors inorder to couple the MR-TOF MS with external ion sources or ion receiversand to avoid beam passage through fringing fields of mirror edges.

The invention is applicable to various ion sources, including pulsed ionsources, like MAIDI or SIMS, quasi- continuous ion sources, like MALDIwith collisional cooling, as well as intrinsically continuous ionsources like ESI, EI, CI, PI, ICP or a fragmenting cell of a tandem massspectrometer. All continuous or quasi-continuous ion sources preferablyoperate with an ion guide.

As mentioned earlier, having a much wider acceptance, the MR-TOF MS ofthe invention can be used in conjunction with an ion storing device,avoiding ion losses between infrequent accelerating pulses. Such ionstoring can occur in gas filled radio frequency (RF) storing devices ofvarious kinds, including ion guides, RF channels, ring electrode traps,wire guides, IT or LIT, incorporated either into an ion source itself orinto an accelerator of the MR-TOF MS. The invention employs either:

-   -   a direct acceleration out of an ion storing device, axial or        orthogonal,    -   or a dual acceleration scheme, where slow ion pulse is ejected        out of the storing device with consecutive pulsed acceleration,        axial or orthogonal, such accelerator may be made either as a DC        accelerator or an RF ion guide switching between RF transmitting        mode and DC pulsing mode,    -   or a dual storage scheme, where slow ion pulses are released        from a first storing trap and admitted into the second trap        usually operated at a lower gas pressure.    -   Ion ejection out of the second storing device can be also made        axially or orthogonally, or via an additional accelerator, axial        or an orthogonal.

Some compromises in parameters of ion packets are acceptable because ofsubstantial extension of flight path and wide acceptance of the novelMR-TOF MS.

The preferred embodiment of the invention employs the latter- morecomplex, but advantageous scheme of dual ion storage. Ion guides arepreferred choice for both storage devices. It is preferable using anadditional set of pulsed electrodes, whose field well penetrates intoion storage area of the second ion guide and allows fast ion ejection inaxial direction with a small turn around time, while providing fairlyuniform accelerating field and a moderate ion divergence. Compared toorthogonal acceleration scheme the invention provides an almost completeutilization of continuous ion beam. Some increase of the turn aroundtime is compensated by an extension of the flight path.

The invention suggests several novel ion storing devices, such as ahybrid ion trap, composed of ion guide and a 3-D ion trap with an openring electrode. Simulations of the segmented analog have shownfeasibility of such trap for preparation of ions for MR-TOF analysis.Another novel device comprises a linear ion trap with auxiliaryelectrodes. Both ion trapping and axial ejection could be achieved bypulsing voltages on separate set of electrodes, and not having any RFsignals on them.

The invention is expected to provide more intense ion pulses and as aresult dynamic range and life time of the ion detector become animportant issue. Multiple solutions are known in the art, including ionsuppression either at ion storage, or mass separation or detectionstages. The known strategies include automatic adjustment of ionintensity or mass filtering of unwanted beam components. Dynamic rangeis enhanced by using a secondary electron multiplier (SEM) and analog todigital converters (ADC) for data acquisition. A specific of theinvention is in longer pulse duration, allowing lower bandwidth andsomewhat easier solutions of the above problems.

The scheme is expected to provide a complete utilization of continuousor quasi-continuous ion beam as well as an improved resolution, in therange of R˜100,000. The MR-TOF MS could be used either as a stand-aloneinstrument, or as a part of LC-MS or MS-MS tandem, first of all expectedas a second analyzer of fragment ions, combined with any know massseparator of parent ions and a with any known kind of fragmenting cell.

The MR-TOF MS of the invention could be also used as a first, separatingmass spectrometer in a tandem mass spectrometer arrangement. Theadvantage of using MR-TOF becomes apparent in a co-pending patent by oneof the authors. The co-pending invention suggests using slow TOF1 forion separation, combined with a fast TOF2 for fragment analysis. Thearrangement allows parallel analysis of multiple precursors per singlepulse out of ion source. Current invention allows particularly longseparation in MR-TOF MS, as well as separation at low and medium energyof ion beam, tight focusing of the beam and precise control of ion beamlocation, useful while directing the beam into a fragmenting cell.

An enhanced transmission and enhanced resolution of MR-TOF could be alsoused in both stages of mass spectrometric analysis. In this case aprolonged flight time in the second shoulder requires selection of asingle precursor by a timed ion selector, thus loosing opportunity ofparallel MS-MS analysis, but instead providing for high specificity,resolution and mass accuracy of MS-MS analysis. Multi-stage MSn analysiscould be accomplished in an instrument with a single MR-TOF analyzer.For example, the same analyzer could be used both for parent separation,daughter separation and grand-daughter ion analysis if the collisionalcell reverts direction of ion flow and timed ion selector is usedbetween MR-TOF and fragmentation cell. Ions are passed between MR TOFanalyzer and collisional cell back and forth.

Both modes of parallel MS-MS analysis and of high resolution MS-MSanalysis could be accomplished in a single versatile instrument byadjusting flight path and acceleration voltage, preferably on bothMR-TOF. Reducing voltage in a first analyzer and reducing flight path(by pulse deflecting ion beam and using fewer reflections) in the secondanalyzer would provide such versatility.

Ceriainly, the utility of MR-TOF MS of the invention spreads onto a muchwider variety of devices and methods. As an example, MR-TOF MS could becombined with any up-front sample separation in various types ofchromatography, or mass spectrometric separation in any type of externalmass spectrometer or ion mobility spectrometer. A variety of gas filledstorage devices and gas filled fragmentation cells employed in variousembodiments could be as well converted into gaseous ion reactors. Suchreactors could be useful for example for employing ion-molecularreactions in ICP method to enhancing isotopic sensitivity, could beusing ion-ion reactions between multiply charged ions and ions of theopposite polarity, either for charge reduction or selectivefragmentation, so as such reactors could be used for electron capturedissociation of multiply charge ions.

BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the present invention, reference isnow made to the following drawings in which:

FIG. 1 shows a multi-reflecting time-of-flight mass spectrometer (MR-TOFMS) of prior art, by Wollnik et al, GB patent No 2080021 (FIG. 3 andFIG. 4 of the GB patent).

FIG. 2 shows a ‘folded path’ MR-TOF MS of a prototype by Nazarenko etal., SU1725289.

FIG. 3 shows a ‘coaxial reflecting’ MR-TOF MS of prior art by M. Park,U.S. Pat. No. 6,107,625.

FIG. 4 shows a schematic of the preferred embodiment of the MR-TOF MS ofthe invention, with details on novel periodic lenses.

FIG. 5 shows MR TOF analyzer geometry and potentials of ion mirrors ofthe preferred embodiment of the invention.

FIG. 6 shows a schematic and principles of ion path extension by edgeion reflections in the shift direction.

FIG. 7 shows a generalized schematic of ion sampling from continuous ionsources into the MR-TOF MS of the invention using an intermediate ionstorage device, wherein:

FIG. 7A shows a block diagram of the pulsed ion source in the MR-TOF MS;

FIG. 7B shows details of the electrospray ion source as an example ofthe continuous ion source;

FIG. 7C shows details of the MALDI ion source with collisional dampeningas an example of the quasi-continuous ion source;

FIG. 7D shows details of the intermediate storage ion guide;

FIG; 8 shows a schematic of a second ion storage device and of the ionaccelerator;

FIG. 9 shows a block diagram of dual ion storage with axial ejection andwith an optional accelerator;

FIG. 10 shows a particular arrangement of a second storage deviceproviding a pulsed axial ion ejection.

FIG. 11 shows an arrangement with orthogonal acceleration out ofnon-storing ion guide

FIG. 12 shows a particular arrangement of the second storage deviceforming a hybrid of a quadrupole ion guide and 3-D quadrupole ion trap.

FIG. 13 shows a segmented analog of the hybrid trap.

FIG. 14 shows the detailed schematics of the preferred embodiment ofMR-TOF MS of the invention.

FIG. 15 shows the schematics of the preferred embodiment of tandem massspectrometer with parallel MS-MS analysis and including MR-TOF MS as afirst MS stage of slow separation of parent ions.

FIG. 16 shows the schematics of the preferred embodiment of tandem massspectrometer with MR-TOF MS at both MS stages providing a versatileswitching between high throughput and high-resolution modes of MS-MSanalysis.

FIG. 17 shows the preferred embodiment of mass spectrometer formultistage MSn analysis, and employing a single MR-TOF MS analyzer and afragmentation cell, reverting ion flow.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

The present invention relates generally to the area ofmass-spectroscopic analysis, and more particularly is concerned with theapparatus, including a multi reflecting time-of-flight mass spectrometer(MR TOF MS). More specifically, the invention improves resolution andsensitivity of planar and gridless MR-TOF MS by employing a novelarrangement and control of mirror electrodes in combination with aperiodic set of lenses in a drift space. Because of improved spatial andtime focusing, the MR-TOF MS of the invention has a wider acceptance andconfident confinement of ion beam along an extended folded ion path. Asa result, the MR-TOF MS of the invention can be efficiently coupled tocontinuous ion sources via an ion storage device, thus saving on dutycycle of ion sampling. The MR-TOF MS of the invention is suggested foruse in tandem mass spectrometers, either as a first slow separator intandems with two-dimensional parallel MS-MS analysis or as a tandememploying MR-TOF MS at both stages of analysis.

FIG. 1 shows a multi-reflecting time-of-flight mass spectrometer (MR-TOFMS) of prior art, by Wollnik et al., GB patent No 2080021 (FIG. 3 andFIG. 4 of the GB patent). In a time-of-flight mass spectrometer ions ofdifferent masses and energies are emitted by a source 12. The flightpath of ions to a collector 20 is folded by arranging for multiplereflections of the ions by mirrors R1, R2, . . . Rn. The mirrors aresuch that the ion flight time is independent of ion energy. The patentshows two geometrical arrangements of multiple axially symmetric ionmirrors. In both arrangements ion mirrors are located in two parallelplanes I and II and are aligned along the surface of ion path. In onearrangement this surface is a plane and in another one it is a cylinder.Note that ions travel at an angle to optical axis of ion mirrors whichinduces additional time-of-flight aberrations and thus considerablycomplicates achieving high resolution.

FIG. 2 shows a ‘folded path’ MR-TOF MS of a prototype by Nazarenko etal., described in Russian patent SU1725289. The MR-TOF MS of the patentcomprises two gridless electrostatic mirrors, each composed of threeelectrodes 3, 4 and 5 for one mirror, and 6, 7 and 8 for another mirror.Each electrode is made of a pair of parallel plates ‘a’ and ‘b’,symmetric with respect to the ‘central’ plane XZ. A source 1 andreceiver 2 are located in the drift space between the said ion mirrors.The mirrors provide multiple ion reflections. Number of reflections isadjusted by moving the ion source along the X-axis relative to thedetector. The patent describes a type of ion focusing which is achievedon every ion turn, achieving a spatial ion focusing in Y direction and asecond order time of flight focusing with respect to ion energy.

Note that the prototype provides no ion focusing in the shift direction,thus essentially limiting the number of reflection cycles. It also doesnot provide time-of-flight focusing with respect to spatial ion spreadin Y direction. Therefore, the MR-TOF MS of the prototype failsdelivering wide acceptance of analyzer and thus an ability of workingwith real ion sources. Finally, the prototype has no implication on thetype of ion source, and on efficient ways of coupling of MR-TOF MS tovarious ion sources.

FIG. 3 shows a ‘coaxial reflecting’ MR-TOF MS of prior art by M. Park,U.S. Pat. No. 6,107,625. The invention comprises two electrostaticreflectors 34 and 38, positioned coaxially with respect to one anothersuch that ions generated by an ion source 32 can be reflected back andforth between reflectors. The first reflecting device 34 combinesfunctions of an orthogonal accelerator and of an ion mirror. Aftermultiple ion reflections either of mirrors is rapidly switched off toallow the ions to pass through the reflector and onto an ion detector36. The patent teaches a way of coupling of continuous ion source to anMR-TOF MS. The described apparatus indeed achieves high resolutionwithin a small size instrument. However, an employed ‘coaxialreflecting’ scheme strongly reduces mass range and decreases the dutycycle of ion sampling from a continuous ion beam. Meshes causesubstantial ion losses. Duty cycle is improved in a later work by authorafter introducing a storing linear ion trap (LIT) into the ion source.

FIG. 4 shows a schematic of the preferred embodiment of the MR-TOF MS ofthe invention, with details on novel periodic lenses. The MR-TOF MS 11comprises a pulsed ion source 12 with a built in accelerator 13, an ionreceiver 16, a set of two gridless ion mirrors 15, parallel to eachother and substantially elongated in a ‘shift’ direction, denoted hereas Y axis, a field-free space 14 between the said mirrors and a set ofmultiple lenses 17, positioned in the said drift space.

The above elements are arranged to provide a folded ion path 19 betweenthe ion source 12 and the ion receiver 16, the said ion path beingcombined of multiple reflections between the ion mirrors 15 and of anion drift in the shift Y direction. The shift is arranged by slighttilting, mechanically or electronically, of the incoming ion packetswith respect to the X-axis. The lenses 17 are positioned along theY-axis with a period corresponding to ion shift per integer number ofion reflections. The preferred embodiment strongly enhances acceptanceof the MR-TOF MS by providing novel ion optics properties—periodicfocusing by lenses 17 in the shift Y direction, complementing a periodicspatial focusing in the orthogonal Z direction, provided by planargridless ion mirrors. Those ion optics properties as well as improvedtime-of-flight focusing by specially designed ion mirrors of theinvention are discussed below in more details.

Incorporation of periodic lenses is a completely novel feature in MR-TOFMS, which provides stable retention of the ions along the main jigsawfolded ion path. The lens tuning allows periodic, repeatable focusing ina shift direction, achieved when focal length F matches an integernumber of half reflections or quarters of full ion turns (P/4), F=N*P/4.The tightest focusing occurs when F=P/4. Such tight focusing isadvantageous for minimizing shift per turn and making instrumentcompact. It is important that even under the condition of such tightfocusing lenses remain weak because of a relatively long ion path perturn, and therefore they introduce only minor incorrigibletime-of-flight aberrations with respect to the ion spatial spread in theplane of the folded ion path. Preferably lenses are lenses, i.e.substantially elongated across the plain of ion path, to provide anadvantage of fairly independent tuning of spatial focusing by ionmirrors and lenses across the plane of the folded ion path and in thisplane, respectively. Such lenses may also incorporate steering by usingasymmetric voltages on the side plates.

The set of periodic lenses brings the novel quality to MR TOF: the ionbeam remains confined even after an extremely large number ofreflections (actually achieved if using reflections in the shiftdirection). Even more, using ion optics simulation the inventors foundout that ion motion in the novel MR-TOF efficiently withstands externaldistortions, like inaccuracies of geometry, stray electric and magneticfields of surfaces, pumps and gauges, as well as space charge of the ionbeam. The MR-TOF returns ions into vicinity of main trajectory in spiteof those distortions. This effect is equivalent to trapping in thepotential well. The feature of periodic lenses allows compact packagingof MR-TOF MS with an extended flight path, combined with confident fulltransmission of ion beam.

FIG. 4 also shows a side view 21 of the same preferred embodiment aswell as an axial potential distribution 22 in the analyzer of thepreferred MR-TOP MS. Preferably, the mirrors 15 are symmetric withrespect to the XY plane and preferably, though not necessarily,identical with respect to each other, i.e. are symmetric around the YZplane. Preferably, the mirrors 15 are composed of at least 4 electrodes,comprising a lens electrode 15L, two electrodes 15E and a cap electrode15C in addition to a specially formed edge of the drift space 14. Asmentioned, the mirrors are substantially elongated in a shift direction,forming a two-dimensional electrostatic field around the area of thefolded ion path 19.

Novel focusing properties of the mirrors in the invention are providedby choosing a proper distance between the mirrors and adjustment ofelectrode potentials. The inventors have found such parameters by ionoptics simulations with a built-in calculation of derivatives and alsowith a built-in automatic optimization block. Working with such aproprietary program, the inventors have formulated some general trendsof optimization algorithms and several key requirements to the ionoptics of ion mirrors. For example, for symmetric MR-TOF MS with twoidentical mirrors, each mirror should comprise at least 4 electrodes inorder to have 5 independently tuned parameters:

-   -   a) 3 parameters (optimally two electrode potentials and the        drift length between the mirrors) are chosen to provide a        periodic (after each reflection) third-order time-of-flight        focusing with respect to energy, i.e. the tuning allows        eliminating the first, second and third-order derivatives of the        ion flight time on the ion energy;    -   b) one parameter (optimally the potential of the ‘incorporated        lens’ electrode closest to the drift space) provides a so-called        ‘parallel-to-point’ spatial focusing across the plane of the        folded ion path. Such term means that a parallel ion packet,        starting in the middle of drift space, will be focused into a        point after half a turn and will be converted back into a        parallel ion packet after a full turn. Advantageously this        focusing is arranged so that ions of the packet also intersect a        plane of ion path in the vicinity of turning point;    -   c) one remaining parameter is adjusted to eliminate the        second-order derivative of the flight time of the just mentioned        ion packet with respect to the initial ion offset from the plane        of the folded ion path.

If both conditions (b) and (c) are satisfied, then the symmetry of themirror arrangement automatically leads to elimination of alltime-of-flight aberrations up to the second order on the initialcoordinate and angular spread across the plane of the folded ion pathafter each full turn, i.e. after an even number of reflections.

The inventors realized that elimination of high-order time-of-flightaberrations is stable with respect to assembly defects as well as tomoderate variations of the drift lengths and electrode potentials.Therefore, a high resolving power could be obtained by tuning of novelMR-TOF MS while adjusting only one electrode potential, in fact, varyingone parameter—a linear dependence of the ion flight time on the ionenergy.

FIG. 5 shows particular examples of geometry and voltages of MR-TOFanalyzer of the invention; which provide the previously described highorder spatial and time-of-flight focusing. The view 23 shows dimensionsof the particular four-electrode mirror with dimensions being normalizedto a length L of typical electrode. The electrodes of the mirror aredenoted as 15L for lens electrode, 15E for two middle electrodes and 15Cfor a cap electrode. Similarly, view 24 shows dimensions of the driftspace and of the entire mirror, while view 25 shows potentials onelectrodes of the same particular MR-TOF MS. The potentials arenormalized to the nominal energy E of the ion beam. The analyzer formsan axial potential distribution similar to one shown on the view 22 ofFIG. 4.

The elongated two-dimensional structure of ion mirror could be formedusing electrodes of various shapes. The view 26 of FIG. 5 shows fewpossible types of electrode geometry, including elongated square frames,thin plates with elongated slots, square bars and not shown types formedby parallel rods, curved electrodes, ‘like cones, hyperbolas, etc.’ Theinventors also expect that a desired structure of electric field couldbe synthesized using less number of two-dimensionally shaped electrodes.

To preserve a two-dimensional field structure, a special treatment of aboundary problem is required. To avoid distortions of the fieldstructure the mirrors are either made much longer than the total shiftof the folded ion path, or employ special devices, like for example afine-structured printed circuit boards (PCB) 30 with a shape ofelectrodes repeating a shape of equipotential lines of the mirror field.In our ion optics simulations we found that a simple adjustment of widthof the lens edge allows noticeable reduction of fringing fieldpenetration. Similar results could be obtained by introducing anadditional edge electrode, for example as a rib of the lens electrode15L.

FIG. 6 shows a schematic and principles of ion path extension by ionreflections in the shift direction within the MR-TOF analyzer of thepreferred embodiment of the invention. In addition to standardcomponents, which are shown using previous numbers, the embodiment 31comprises steering devices 32 and 33 and an optional in-line ionreceiver 34. The incident ion packet 35 can be either deflected onto anadditional detector 34 or steered into the MR-TOF MS along the foldedpath 36. On the other end of the shift axis Y the second steering device33 can either release ions onto the ion receiver 16 along the trajectory38 or steer the ion packet again into the MR-TOF MS along the folded ionpath 37.

In operation, in a particular regime, when the entrance steering 32 isdisabled and the exit steering 33 is constantly on, the MR-TOF MSretains a non-repeating folded ion path and thus retains full mass rangeof mass spectrometric analysis, while doubling the flight path. Theentrance steering can be used to by-pass analyzer all along. Suchfeature appears useful in a co-pending patent, where the MR-TOF MS isused as an ion separator of a tandem MS and the bypass feature wouldallow toggling between tandem and MS-only regimes.

The steering could be used to pass ion packets along a repetitive,cyclic folded ion path, wherein an increase of flight path isaccompanied by a proportional shrinking of mass range, a compromise tobe made upon requirements of a particular application. In this case thesteering device 32 can be used also as an ion gate for choosing adesired part of the analyzed mass spectrum

Geometrical constrains of the entire analyzer and a fringing field ofmirror edges may become important while using reflections in the driftdirection. An optional way around the problem is in passing the ion beamthrough ion mirrors, more specifically, through the slit in the mirrorcap electrode 15C. The mirror 15 then can be extended by adding separateelectrodes, e.g. as shown by dashed line, and should be turned on andoff in a pulsed mode.

A particular example 41 of steering device is shown also on the FIG. 6.The steering device 41 comprises a set of parallel plates 42 to 46,where plates 42 are grounded. The device combines feature of planardeflecting plates and of a planar lens. The device could be eithertoggled between two functions or could combine two functionssimultaneously by tuning voltages on plates 44 and 45. The device allowsincorporation into a periodic structure of lenses. In this case, eachindividual cell could be used for both ion focusing and/or reflection ina drift direction. Deflection plates could operate constantly or in apulsed mode to allow ion gating, selecting narrow mass range, andanalyzing multiple precursors or multiple mass windows simultaneously.Flexible switching between lenses and deflectors is also useful whileovercoming the problem of fringing fields, since the deflectors cancreate a closed loop ion trajectory, staying well within boundaries ofthe unaffected mirror field (not shown).

Introduction of ion deflection causes compromises in time-of-flightresolution; hence they are generally used for ion manipulation,extension of flight time, rather than for improving resolution of theMR-TOF MS.

For example, with a typical energy spread of 5% and the phase space ofthe beam of 10π mm mrad in both directions normal to the beam path, anion optical simulations of the MR TOF MS of the invention with L=25 mmpredict the achievable mass resolving power (FWHM) of 100,000 withoutusing deflectors in the mode with the maximal focal length of thelenses, equal to the length of the full beam turn (two reflections).With the tightest focusing induced by lenses and additional use ofdeflectors, this resolving power is expected to drop down to 30,000.Note however that because of the extended flight time this value can beachieved for much more relaxed values of the ion turn around time ascompared to the conventional TOF MS with the same resolving power.

Now that we have completed a description of the MR-TOF MS of theinvention it is of particular importance to note, that the novel MR-TOFanalyzer has a much higher tolerance to spatial and temporal spreads ofion beam. The novel analyzer provides a stable ion beam confinement,which allows an extension of flight time without causing geometrical ionlosses. An extended flight time, in turn, enhances TOF resolution andreduces the effect of ion turn around time, appearing in the pulsed ionsource. Finally, the MR-TOF MS of the invention also provides a highorder time-of-flight focusing with respect to the spatial spread ofinitial ion beam, i.e. much wider beams can be accepted without loosingtime-of-flight resolution. On the other hand, an extension of flighttime reduces efficiency of ion sampling out of continuous ion beams.Though the invention may be used with a pulsed ion sources likesecondary ionization mass spectrometry ion source (SIMS) or matrixassisted laser desorption (MALDI), a long-term stability of excited ionsmay become an obstacle. Stability of those ions may be improved by gasdampening from a pulsed gas supply. Even with a pulsed acceleration ofsuch ions the duration of ion pulse becomes to large to consider thosesources as pulsed. The contradiction is resolved with the introductionof another key feature of the invention—incorporation of ion storing andpulse ejection into a continuous or quasi-continuous ion sources, likeelectrospray (ESI), atmospheric pressure chemical ionization (APCI),electron impact (EI), chemical ionization (CI), photo ionization (PI),inductively coupled plasma (ICP), a gas filled MALDI, as well as iongaseous reaction cells or a collisional cell of any tandemmass-spectrometer.

The invention strongly improves efficiency of ion sampling into anMR-TOF MS by adding an ion storing step for accumulation of continuousion beam and pulsed ion ejection at a reduced frequency, correspondingto an extended flight time of the MR-TOF MS. Such ion storing occurs ingas filled radio frequency (RF) storage devices of various kinds,including ion guides, RF channels, IT or LIT, wire or ring electrodetraps, incorporated either into an ion source itself or into anaccelerator of the MR-TOF MS. The storage devices of the art are gasfilled for ion dampening at gas pressure sufficient for hundreds of ioncollisions with gas molecules. Those devices employ radio frequency (RF)field for ion radial confinement and axial static or moving waveelectric fields for controlling axial ion motion. The storing stepavoids ion losses between rare pulses of any MR-TOF MS.

In reference to FIG. 7A, and using a block diagram level of detailing,the pulsed ion source in the—MR-TOF MS of the preferred embodiment ofthe invention 51 comprises a continuous ion source 61, a storing ionguide 71, a second storage device 81, an accelerator 91, beingsequentially interconnected. The pulsed ion source 51 is connected tothe MR-TOF 31. The block diagram shows the most general case, whereinelements 71, 81 and 91 are optional, i.e. could be either omitted ormerged together within some particular embodiments.

In operation, the continuous ion source 61, preferably gaseous ionsource, generates a continuous ion beam, which is preferably transportedwithin an ion guide 71. Preferably, the ion guide 71 stores continuousion beam and ejects ion packets periodically with a period correspondingto that of the MR-TOF analyzer 31. Such ejected ion packets are passedinto the accelerator 91, either directly or via an optional, secondstorage device 81. The accelerator, continuous or pulsed, inject fastion packets into the MR-TOF analyzer, axially or orthogonal. Both, theion guide 71 and the second storage device 81 could be any RF confiningand gas filled device as illustrated by the following list: 3-D iontrap, quadrupole, multipole or wire ion guide, RF channel, ringelectrode trap, ion funnel or a linear ion trap.

The major function of an additional storing device 81 is to prepare anion cloud at different conditions compared to the rest of ions, storedin the first storing ion guide 71. Such conditions may differ by gaspressure, space charge or mass composition of ion beam or byconfiguration of ejecting electrodes. As it will be shown in thefollowing description, the dual storage scheme is more flexible, allowsfull utilization of ion beam and a number of automatic adjustments. Mostimportant, it generates ion beam with a smaller phase space and improvesbeam acceptance by analyzer. The advantages of using an additionalstorage device will become apparent in the following detaileddescription of the preferred embodiment of the MR-TOF MS of theinvention, which employs the dual storage scheme.

FIG. 7B shows the particular example 61B of gaseous continuous ionsource—ESI ion source, comprising a spraying probe 62, a sampling nozzle63, a sampling skimmer 64 and pumps 65 and 75. Components and principlesof operation of ESI ion sources are well described in the art. Asolution of analyte compound is sprayed from the probe 62 in the regionwith atmospheric pressure. Highly charged aerosol evaporates, thusforming gaseous ions of analyte, which are sampled via the samplingnozzle 63. The pump 65 evacuates an excessive gas to a gas pressure offew mbar. Ions are further sampled via the sampling skimmer 64 withassistance of gas flow and electrostatic fields, generating a continuousion beam 66, while gas is evacuated by the pump 75.

FIG. 7C shows the particular example 61C of a quasi-continuous, MALDIion source with gas cooling, which comprises a sample plate 67, a laser68, a supply 69 of cooling gas and a pump 75. The MALDI ion source 61Bwith gas cooling generates ions of analyte, while illuminating a sampleon a sample plate 67 by the pulsed laser 68. A supply 69 provides acooling gas around the sample plate at an intermediate gas pressure,about 0.01 mbar (WO9938185) or around 1 mbar (WO0178106). Ions, emittedfrom the sample plate are cooled and stabilized in gas collisions. Ionstability is particularly important for the use in MR-TOF MS, since itemploys a prolonged analysis time. Ions kinetic energy and sharp timingcharacteristics become dampened in gas collisions. The resulting ionbeam 66 is considered more as a quasi-continuous ion beam, rather than apulsed ion beam.

FIG. 7D shows a schematic of an intermediate storing ion guide 71. Bothof earlier described ion sources 61B and 61C are connected to an ionguide 71. The particular example 71 of the storing ion guide comprisesquadrupole rods 72, supplied with radio frequency (RF) voltage, a set ofsupplementary electrodes 73, an exit aperture 74 and a pump 75. Note,that the same pump 75 has been shown earlier in FIG. 7B and 7C. Inoperation, either continuous or quasi-continuous ion beam 66 is directedinto the ion guide 71. Ions are sampled via an aperture 64, while thepump 75 evacuates an excessive gas. The aperture 64 and the pump 75 aresimilar in cases of both ion sources, because of about equal gaspressure in front of the aperture 64. Ions are accumulated between RFrods 72, while being dampened in gas collisions and being retarded byapertures 64 and 74. Ions are confined near the axis of RF quadrupoleand in the bottom of DC potential well. Periodically ion packets 76 arepulse ejected out of the storing ion guide and into the accelerator 91,either directly or via an optional, second ion storage device 81,described below.

The invention may employ an unusual arrangement of ion storing, wheresupplementary electrodes 73 organize axial DC distribution in the ionguide 71. The electrodes 73 surround the RF rods 72, such that theirelectrostatic field efficiently penetrates between the rods. The axialDC distribution is adjusted and varied in time to provide spatiailydistributed ion storage, a controlled ion sampling and a moderateduration of ion ejection process. Note, that manipulations by voltageson the supplementary electrodes 73 do not require any manipulation by RFpotentials on RF rods 72. In fact, it is advantageous to keep RF voltageapplied to the rods 72 in a steady state, thus providing a betterfocused pulsed ion packets. Since ions are ejected along the axis, wherethe RF field is negligible, the RF field has very little affect on axialion velocity. Applying separate RF and pulse signals to different setsof electrodes provides an obvious convenience and ease of makingelectronics supplies.

The storing ion guide 71 can be coupled directly to the accelerator 91,preferably orthogonal. Since the ion guide is filled with gas it ispreferable to provide a soft ion ejection by small modulation ofpotentials on electrodes 73 and 74. Such slow (few to few tenths ofelectron Volts) and fairly long (several microseconds) ion packets arewell compatible with synchronized orthogonal acceleration. The scheme isnot shown since it is fairly common in the prior art (e.g. U.S. Pat. No.6,020,586). The packet 76 passes via an additional differential pumpingstage to accommodate the gas filled ion guide to the analyzer at deepvacuum. The additional stage comprises a lens, forming a nearly parallelion beam. The ion packet enters an orthogonal accelerator 91,synchronously injecting ions into the analyzer. It is preferable using agridless accelerator made of flat plates with slits elongated alongdirection of slow ion beam. An obviously attractive scheme of orientingslits along the shift direction of MR-TOF in fact is inferior to theorthogonal arrangement, wherein the source and slits are oriented andelongated orthogonal to the plane of the folded ion path. Apparently ionfocusing by ion mirrors has a higher (second) order time of-flightfocusing with respect to spatial spread compared to periodic lens havingfirst order focusing if used with a proper compensation by tuning ionmirrors.

The orthogonal accelerator could be either positioned in the drift spaceof the MR-TOF analyzer of the invention, or combined with one of themirrors (or a pulsed portion of one ion mirror) of the planar MR-TOFanalyzer of the invention and operated in a pulse manner. Similarly tothe prior art, the storage ion guide provides an advantage of savingduty cycle of the orthogonal acceleration at the expense of ion massrange.

FIG. 8 shows block diagram of the second storage device 81. The secondstorage device 81 comprises a generic ion trap 82, an exit aperture,either axial 88 or orthogonal 86 and a pump 85. The storage device 81 isconnected the ion guide 71, preferably a storage ion guide. Inoperation, ions are continuously or pulsed injected from the ion guide71 into the generic trap 82. The generic ion trap may be a 3-D ion trap,a linear ion trap formed in quadrupole, a multipole or wire ion guide,preferably equipped with supplementary DC electrodes, RF channel, ringelectrode trap, ion funnel or a combination of those devices. The trapis preferably maintained at a reduced gas pressure about 0.1 mTorr withgas being evacuated by the pump 85. Because of the combined action of RFand DC fields and of the gas dampening, ions are confined near the exitof the trap. Ions are periodically ejected out of the storage device 82directly into the MR-TOF analyzer, either axially 87 or orthogonally 89,via a corresponding aperture, either 86 or 88, serving to reduce gasload onto pumping system of MR-TOF analyzer.

FIG. 9 shows block diagram of dual ion storage with axial ejection andwith an optional accelerator. An optional accelerator 91 comprises a setof electrodes 92, located in the housing 97, which is evacuated by apump 95. In a particular example of FIG. 9 accelerator shares housingand pump with MR-TOF, though they may be pumped differentially toenhance vacuum in MR-TOF. The pulsed ion beam 89 comes out of secondstorage device 81 and is accelerated within a set of electrodes 92.There are numerous types of accelerators described in the art. As anexample, such electrodes may be made of wires, or made of rings orplates with slits or with meshes. They also may comprise electrodessupplied by RF signal to confine ion beam. Ion are accelerated eitheraxially 94 or orthogonally 93 to the direction of ion injection. Theaccelerator operates either continuously or in a pulsed modesynchronized with ion injection. In all cases the accelerator may bearranged and controlled such that the ion package will experience alocal compression 96 at some intermediate time-focusing plane, called anobject plane.

FIG. 10 shows a particular arrangement 101 of a second storage device 81with a pulsed axial ion ejection. The particular second storage device81 comprises a set of multipole rods 102 with short rod extensions 103and an exit aperture 104. The storage device 81 further communicateswith an axial DC accelerator 91, which comprises DC acceleratingelectrodes 105 and an aperture 106.

In operation, ions are formed in an ion source and preferably come viaan intermediate ion guide 71 either as continuous ion source or as aslow ion packet. The second storage device 81 is held at relatively lowgas pressure, say 0.1-1 mTorr, still sufficient for ion corisionaldampening during 1 ms storage time. Rod extensions 103 are supplied withthe same RF signal as rods 102, but kept at a slightly lower DC (10-50Vlower compared to rods 102). Ions are periodically stored and pulseejected out of the second storage device 81 by varying potential on theexit aperture 104. At ion storage stage, the aperture 104 is kept at aretarding potential thus forming a local DC well in the vicinity of exitaperture 103, while still confining ions in radial direction by RF fieldof rod extensions. The sharpness of DC well is adjusted such that ioncloud sizes about 0.5 to 1 mm. At ion ejection stage, the aperture 104is drawn to a strongly negative potential (for positive ions),extracting ions along the axis and out of the second storage device 81.Note that RF field stays on. Since ions are confined near the axis, theyexperience very little effect of RF field during axial ejection. The DCaccelerating electrodes 105 may serve as an energy corrector and a lensfor simultaneous spatial focusing of ion packets 107. An exit aperture106 may be used to reduce gas load on MR TOF MS pumping system. Ourestimates suggest that unless ion cloud would create space chargepotential above 0.5V, parameters of ion packets 107 are well suitablefor MR-TOF MS. At 0.2 eV energy spread, ion cloud diameter 0.5 mm,acceleration potential of 5 kV and 500 V/mm extraction field the ionbeam parameters are: divergence is below 1 degree, energy spread isbelow 5% and turn around time of 1 kDa ions is below 8 ns.

FIG. 11 shows arrangement 111 providing orthogonal ion acceleration outof a non-storing ion guide. The arrangement comprises an ion trap 108, anon-storing ion guide 109 and DC accelerator 91. The arrangement 111could be implemented with various types of ion traps and ion guides. Theparticular ion trap 108 of FIG. 11 is formed by an RF multipole set 112,surrounded by DC electrodes 113 and an exit aperture 114. A particularnon-storing ion guide 109 comprises a multipole set 115 with a slit 117in one of electrodes or an opening between electrodes of RF multipole.The multipole 115 is optionally surrounded by supplementary DCelectrodes 116. Both stages of ion trap and ion guide are pumped withpumps 85 and 95.

In operation, ions are formed in an ion source and preferably come viaan intermediate ion guide 71 either continuously or as a slow ionpacket. The ion trap 108 is held at a relatively low gas pressure, say0.1-1 mTorr, still sufficient for ion collisional dampening during 1 msstorage time. Ions are periodically stored and pulse ejected out of theion trap 108 as a slow ion packet (1-10 us) by modulating potentials ofDC electrodes 113 and of exit aperture 114. The multipole 115 of the ionguide 109 is supplied with RF signal to continue radial ion confinementof axially propagating ion packet. With some predetermined delay to ioninjection pulse a second extraction pulse is applied to multipole rods115 as well as optional pulse may be applied to the supplementaryelectrodes 116. Potentials on multipole 115 are zeroed at apredetermined phase of RF signal (say, at zero volts) and then (after ashort 10-300 ns ‘switch’ delay) switched to some predetermined pulsedpotentials to provide ion bunching and ion extraction in-betweenmultipole rods or through a slot 117 in one of the rods. Ions thenundergo acceleration in the DC stage 91 and enter the MR-TOF MS 31. Thedelay between first pulse ejecting ions out of the ion trap 108 and thesecond extraction pulses in the ion guide 109 is adjusted, such that tomaximize mass range of orthogonally extracted ions.

It should be noted that the storage 103 and accelerator 104 could beconfined in a single unit, with gas extending for the entire length ofrods 112 and 115, whereas aperture 114 and electrodes 113 could beomitted altogether and electrodes 112 and 115 could be optionallycombined into a single set of electrodes.

FIG. 12 shows yet another particular arrangement of the storage device,which may be called ‘a hybrid of ion guide with 3D ion trap’. Referringto FIG. 12, the particular storage device 121 comprises a quadrupole ionguide formed of two pairs of electrodes 122 and 123, and a 3-D Paul trapwith a ring electrode 127 and cap electrodes 126 and 129. The ringelectrode 127 is open with a large size aperture 125. The cap electrode129 has an aperture 130 for orthogonal ion ejection.

In operation, a continuous radio frequency (RF) field spans across theion guide and the 3-D trap. In a simplest mode, pair of electrodes 122is connected to ring electrode 127 and form one pole, which is suppliedwith RF voltage, while pair of electrodes 123 is connected to capelectrodes 126 and 129, forming another pole. The same RF field may beachieved if RF voltage is supplied symmetrically between the above twopoles. In a preferred mode, similar structure of RF field is preserved.However, corresponding electrodes may be supplied with signal of thesame frequency and phase, while having different amplitude of RF voltageand separately controlled DC potentials. Ions are supplied (continuouslyor pulsed) through the ion guide between pairs of electrodes 122 and 123and enter into the 3-D trap via an opening 125.

Distribution of RF and DC potentials form a mass dependent axial barrierbetween linear quadrupole 122-123 and quadrupole trap 126-129 withamplitude in the range of several volts, and inverse proportion to ionmass-to-charge ratio m/z. In general case, the barrier causes ionsharing between the guide and the 3-D trap. By raising DC offset onelectrodes 122-123 and with assistance of gas collisions, majority ofions could be concentrated in the middle of 3-D trap. In a preferredmode the said DC offset is slowly ramped up such that the barrierdisappears for ions above some m/z*. Ions of m/z* pass over the barrierwith a minimum amplitude of secular oscillations in the trap. Slow DCramping allows soft transfer of all ions into the trap. At the sametime, ions coming from the ion source could be stored in theintermediate storing ion guide 71 to improve duty cycle. After ions aredampened in 3-D trap (1-5 ms), RF field could be switched off and aftera short and optimized delay (10-300 ns), a high voltage pulse issupplied to at least some of 3-D trap electrodes 126, 127 and 129, suchthat to eject ion packet via the aperture 130 in the cap electrode 129.In one preferred mode, the RF voltage is replaced by a square wavesignal and the ion ejection pulse is synchronized to a specific phase ofthe square wave signal, such that potential distribution stays constantduring the ion ejection phase.

FIG. 13 shows a segmented analog 131 of the above described hybrid trap121. The pair of quadrupole rods 122 is replaced by a plate 132 with achannel 135. The ring electrode 127 is replaced by a plate electrode 137with a circular hole 138. The pair of electrodes 123 is replaced byplates 133 and 134, symmetrically surrounding plate 132. The capelectrode 126 is replaced by a cap plate 136 and cap electrode 129 withaperture 130 is replaced by a cap plate 139 with an aperture 140. Capplates 136 and 139 are located parallel to plates 133 and 134 or astheir extension. The plates are arranged as a sandwich shown on the leftpart of FIG. 13. The same electrodes are shown separately on the rightpart of FIG. 13.

In operation, the segmented trap 131 provides the same field structurein the vicinity of axis. It is a quadrupolar 2-D field near the axis ofthe channel 135 and a 3-D quadrupolar field near the center of circularhole 138. Trapping field is formed by either RF voltage or square wavesignal applied to plates. RF field provides ion sharing betweensegmented ion guide and segmented 3-D ion trap. Periodically RF signalis switched off at some fixed phase of RF signal (preferably 0V) andafter a predetermined delay (10-300 ns) a high voltage pulse is appliedto electrodes to provide for ion ejection within nearly homogeneouselectric field. Ion packet is extracted via an aperture 140, alsoserving to reduce gas load onto pumping system of MRTOF. Preferably anRF signal is applied only to central plates 135 and 137, a DC ramp isapplied to plates 133 and 134 (or including 132) and high voltage pulsesare applied to plates 136 and 140. Such arrangement allows separatingRF, DC signals and high voltage pulses.

Other embodiments of ion storage 91 may include a linear ion trap formedby coaxial apertures (see e.g. A. Luca, S. Schlemmer, I. Cermak, D.Gerlich, Rev. Sci. Instrum., 72 (2001), 2900-2908), segmented trap withorthogonal ejection (similar to that in U.S. Pat. No. 6,670,606B1),segmented ring ion trap (Q. Ji, M. Davenport, C. Enke, J. Holland, J.American Soc. Mass Spectrom, 7, 1996, 1009-1017), wire traps, traps,formed by meshes surrounded by electrodes with RF signal, helical wiretraps, etc.

FIG. 14 shows the detailed schematics of the preferred embodiment ofMR-TOF MS of the invention. The preferred embodiment 141 of theinvention comprises a multi-reflecting analyzer 31 and a pulsed ionsource 51. As been earlier described the pulsed ion source 51 comprisessequentially connected continuous ion source 61, an intermediate storingion guide 71, a second storing ion guide 81 and an accelerator. Eachmain component comprises earlier described elements. The particularshown example of continuous ion source 61 is an ESI ion source,comprising a spray probe 62, a sampling nozzle 63, a sampling skimmer 64and a pump 65. The intermediate storing ion guide 71 comprises a set ofquadrupole RF rods 72, surrounded by supplementary pulsed electrodes 73,an exit aperture 74 and a pump 75. The second storing ion guide 81comprises a gas confining cap 82, a set 83 of quadrupole RF rods,surrounded by a set 84 of supplementary pulsed electrodes, an exitaperture 88, a pump 85. The accelerator 91 comprises a set of electrodes92, a housing 97, shared with the MR-TOF MS analyzer and a pump 95. TheMR-TOF analyzer 31 comprises a field free region 14, two planar andgridless ion mirrors 15, an in-line ion detector 34, a set of periodiclenses 17, a set 32 of entrance steering plates, and a set 33 of exitsteering plates.

In operation, the ESI ion source 61 generates the continuous ion beam66, which is stored in the storing ion guide 71 at an intermediate gaspressure (from 0.01 to 0.1 mbar). The intermediate storing ion guide 71periodically ejects slow ion packets into the second storing ion guide81, which operates at a lower gas pressure (preferably from 10-4 to 10-3mbar). A gas confining cap 82 allows having a higher gas pressure in theupstream area of the second ion guide 81, thus improving ion dampeningand ion trapping at a smaller gas pressure near the exit of the guide.This helps reducing gas load onto a pump 95 and, thus, helps keeping lowgas pressure in the chamber 97 of MR-TOF analyzer 31 and accelerator 91,MR-TOF normally requires a lower gas pressure (below 10-7 mbar) becauseof the extended flight path, compared to conventional TOF MS.

The slow ion packet contains a fixed portion of all ions accumulated inthe first ion guide 71. As a guiding example, approximately 10% ofstored ions are sampled through the aperture 74 in about every 1 ms.Such balance between coming and leaving ions allows refreshing of theion content in every 10 ms. The amount of ions, stored in the first ionguide 71, depends on intensity of ESI in beam. At a typical ion flow of3.108 ions a second the first ion guide 71 would contain about 3.106ions, known to build up a noticeable space charge field. With only 10%of ions being sampled into the second storage the amount of ions in thesecond storage is about 3.105. Such ion cloud, being stored in 1 mm3volume would create about 30 meV potential of space charge, being closeto thermal energy (gas kinetic energy of 25 meV) and moderatelyaffecting ion initial parameters. The dual storage scheme providesseveral advantages. First, pulsed injection into the second storingquadrupole ensures a complete ion dampening at low gas pressure. Second,the amplitude of RF signal in the first quadrupole may be adjusted tooperate as a low mass filter. By removing most of solvent ions andchemical background ions the space charge is further reduced. Third, byusing selective excitation of secular ion motion one can also achieve aselective removal of the most intense ion species, building up spacecharge and saturating the detector. Besides, by adjusting the durationof ion injection one can control intensity of ion beam. It helpsimproving dynamic range of data acquisition and in avoiding saturationof the detector.

The first ion guide 71 ejects slow ion packets by a very gentle pulsedaxial field, generated with assistance of pulse potentials on the exitaperture 74 and optionally on the additional electrodes 73. The use ofthe set 73 of additional electrodes allows an accurate control of energyand amount of ejected ions within the packet. The ejected ion packet isalmost completely trapped in the second storing ion guide 81, using apulsed trapping scheme. In more details, a potential on exit aperture 88forms a repelling DC barrier, while RF field of electrodes 83 confinesions in radial direction. Ion packet gets reflected from the far end 88,however, by the time ions will return to the entrance (74) of the secondguide 81, they will see a repelling potential of electrode 74, which wasraised after the completion of ion ejection from the first ion guide 71.Ion kinetic dampening is accelerated because of a higher gas pressure inthe beginning of the ion guide 83. The local increase of gas pressure isformed by gas confining cap 82 and by a gas jet, emerging from theaperture 74.

Trapped ions get confined in the DC potential well, formed with the aidof additional electrodes 84. Such electrodes surround RF rods 83 of thesecond ion guide 81, such that to make an effective and symmetricpenetration of potentials of the additional electrodes. Referring to theelectrostatic field on the axis of the ion guide 81, a set of additionalelectrodes 84 forms an axial distribution of DC field while generating amoderate octapole DC field in the radial direction. It is important tokeep such octapole DC field small enough to avoid ion instability duringa long term storage. As a numeric example, an RF potential of 1.5 kV and3 Mhz frequency is applied to 5 mm quadrupole rods positioned on 10 mmdiameter between centers, Each additional electrode is formed as a platehaving central hole of 5 mm and 7 mm holes for rods. About 20% ofpotential of such plate penetrates to the center of quadrupole assembly.Three plates are located 3 mm apart from each other and 5 mm away fromthe exit aperture. By applying 10V drop to the central plate we form aDC well of c.a. 2V deep. Ions with energy of 100 meV are confined intocloud of c.a. 1 mm long and fraction of mm in diameter. The arrangementhas very little effect on ion stability and allows storing of ionswithin at least one decade of mass to charge ratio.

After collisional dampening and confinement in the ion guide 81 the ionpacket get axially ejected (in the X direction) into the DC accelerator92 and then into the MR-TOF analyzer 31. After emptying of secondstorage the pulsed potentials are returned to their trapping state toprepare for the next cycle of ion storage. The pulsed ejection is madewith the aid of high voltage electric pulses, applied to the set 84 ofadditional electrodes and to the exit aperture 88, while keeping RFpotentials unchanged. Low gas pressure in the second storing quadrupole81 helps avoiding gas discharges while applying high voltage pulses.Since all the ions are stored in the small volume, such pulses do notspill any other ions and pulse amplitude could be fairly high—enough tonoticeably reduce ion turn around time. Thus, the ability of compressingion packet into a small cloud and the ability of applying high voltageaccelerating pulses are, in fact, another two important reasons for dualstorage arrangement. Such ion packet parameters could not be achieved incase of fast ejecting directly out of the first ion guide 71.

Application of fairly large ejecting pulses causes a substantialreduction of ion turn around time and thus allows using an ion guidedirectly as a pulsed ion source for MR-TOF MS. In our ion opticssimulations, made for the above geometrical example, we found that byapplying high voltage pulses to the additional electrodes the turnaround time could be reduced to few nanoseconds. For example, byapplying 5 kV pulse to the middle additional electrode (out of three)and −1 kV pulse to exit aperture, an axial field reaches c.a. 200 V/mm.Assuming 200 meV initial energy spread and 1 mm size of stored ioncloud, the turn around time of 1000 amu ions is 10 ns only and theenergy spread of ejected ion packets is below 200 eV. By applying a c.a.4 kV DC post—acceleration in the DC accelerator 92 the ion beam has lessthan 5% energy spread, is well focused and has a phase space below10π*mm*mrad, which is well compatible with the wide acceptance and highorder time-of-flight focusing of the MR-TOF analyzer of the invention.

In ion optics simulations by inventors the resolution of the MR-TOF MSappears to be mostly limited by turn around time. As a numericalexample, ions of 1000 amu, accelerated to 4 keV energy and Velocity3×104 m/s have 10 ns turn around time, while having 1 ms flight time in0.25 m wide analyzer with 50 reflections (25 reflections while shiftingin one direction and 25 reflections on the way back). Such analyzerprovides a folded path with the effective flight path of 30 m. If 10 nsturn around time is indeed the only limiting factor, then resolutionreaches R=50,000. Further extension of flight time is expected toimprove resolution even more. A longer accumulation would cause somedeterioration of the turn around time. However, the increase of spacecharge field and of the turn around time is expected to be slower thanthe increase of flight time.

Increasing storage time stresses the dynamic range of the detector. Withan increased time-of-flight in MR-TOF and more efficient ionutilization, ions from up to 1 ms accumulation arrive to detector inshort packets of 10-20 ns duration. To avoid saturation of detector andtherefore loss of analytical parameters (such as mass accuracy, massresolution, dynamic range, etc.), one may enhance dynamic range ofdetector by using a secondary electron multiplier (SEM) combined withanalog-to-digital converter (ADC), rather than micro-channel platedetector (MCP) combined with time-to-digital converter (TDC). As one ofembodiments, a hybrid detector could be employed, wherein a singlemicro-channel or micro-sphere plate is followed by a scintillator andphotomultiplier. It is also proposed to use any combination of thefollowing measures:

a) using SEM with two collectors sampling electrons at different stagesof amplification or

b) using an arrangement with dual SEM combined with a rapid steeringdevice and/or

c) using dual amplifiers connected to a pair of acquisition channelsand/or

d) alternating between two different storage time in the intermediate orsecond storing trap, such that intensity of ion pulses varies betweenshots.

Note that MR-TOF is expected to have longer ion pulses (10-20 ns),compared to conventional TOF (1-3 ns). Lower bandwidth requirements makeit easier to implement the means mentioned above.

Higher efficiency of ion usage in MR-TOF would cause faster aging of thedetector. In order to increase life time of the detector and to enhanceits dynamic range it is also proposed to use a pre-scan of mass spectrumat lowered storage times. From this pre-scan, a list of exceedinglyintense peaks could be deduced and stored in the memory of instrumentcontroller. This list could be used to control a pulsed ion selector.Pulsed ion selector could be incorporated in the detector or any of thedeflectors or lenses or in the drift space of MR-TOF in any of the aboveembodiments. This selector is used to suppress ions with mass-to-chargeratio corresponding to intense ion peaks by deflecting or scattering asubstantial portion of intense packets while they fly through theselector. It is also possible to divert these peaks to another detectorwith a substantially lower gain. Preferred embodiments of the selectorinclude: Bradbury-Nielsen ion gate, parallel-plate deflector, a controlgrid within the ion detector (e.g. a grid between dynodes ormicrochannel plates pulsed to stop passage of secondary electronsthrough it). Suppression of ion intensity may be considered incalculation of actual ion intensity. The number of ions per shot may bethen suppressed at any stage of ion storage or at MR-TOF or at thedetector.

In addition to stressing and aging the detector an excessive amount ofions per pulse (above 2*105) is responsible for build up of space chargein storage devices. Various strategies may include a controlledsuppression of ion beam intensity or a number of ions per pulse atstages of preliminary or secondary ion storage. Such controlledsuppression may include selection of mass range of interest, removal oflow mass ions, mass selective removal of the most intense ioncomponents, for example by exciting their secular motion in RF trappingdevice and causing selective loss of those ions.

The above-described scheme of MR-TOF MS combined with ion trap sourceallows 100% conversion of continuous ion beam into ion packets. Besides,achievable parameters of ion packets allow a complete transmission ofions through the novel MR-TOF MS and if turn around time is the majorlimiting factor then it still allows reaching a 50,000 resolution withina 1 m long instrument. Those parameters exceed resolution andsensitivity of existing o-TOF MS as well as superior to that of theexisting MR-TOF MS

Stable ion confinement in the multi-reflecting analyzer and within a setof periodic lenses improves sensitivity and resolution of MR-TOF andallows a prolonged ion separation. Those properties of novel analyzercould be very useful in tandem mass spectrometer with parallel MS-MSanalysis, described in a co-pending application WO2004008481 of one ofthe authors and incorporated here by the reference. Here we introduce aset of periodic lenses into a first multiple reflecting analyzer ofTOF-TOF tandem, thus improving both sensitivity and resolution ofparallel MS-MS analysis.

Referring to FIG. 15, a preferred embodiment of tandem mass spectrometer151 comprises a pulsed ion source 51, a multi-reflecting massspectrometer 31, a fragmentation cell 152 and an orthogonaltime-of-flight mass spectrometer 161. The above described pulsed ionsource 51 comprises a continuous ion source, a dual storing ion guideand an accelerator. The second storing ion guide is shown here as an RFlinear ion trap 83 with auxiliary DC electrodes 84, set up for axial ionejection. The above described MR-TOF MS 31 comprises a field-free region14, an off-line detector 34, two of planar gridless mirrors 15,preferably containing more than four electrodes, configured andcontrolled to provide high order time-flight and spatial focusing, a setof periodic lenses 17 for stable ion confinement along the folded ionpath and a pair of edge deflectors 32 and 33, preferably incorporatedinto edge elements of periodic lenses 17 and providing extension offlight path by edge ion reflections.

The fragmentation cell 152 is a fast fragmentation cell, described indetails in a co-pending patent application. Preferably the fragmentationcell comprises a short (5-30 mm) RF quadrupole 158 for radial ionconfinement, as well as auxiliary DC electrodes 159 and an exit aperture160 to form a time dependent axial electric field. The quadrupole issurrounded by an inner cell 156, filled with gas at a relatively highgas pressure (0.1-1 Torr) via port 157. To reduce gas load on MR-TOF thespace around the cell 156 is pumped by turbo pump 155. To enhance iontransmission the inner cell is supplied with focusing lenses 154 on bothends.

The orthogonal TOF 161 is a conventional device, well described in theart. It comprises an orthogonal acceleration stage 163 with a pulsingelectrode 162 and an in-line detector 164, a pump 165, an electricallyfloated field free region 166, an ion mirror 167 and a TOF ion detector168. The orthogonal acceleration is preferably made of flat electrodeswith slits oriented along the entering ion beam. The orthogonal TOFdiffers from most conventional instruments by a shorter ion path(0.3-0.5 m) and a higher acceleration voltage (above 5 kv) to providefor a fast fragment analysis at about 10 us time. In operation, pulsedion source 51 periodically (say, once per 10 ms) generates bursts ofparent ions, converting continuous ion flux from ion source 61 into ionpulses by storing and ejecting ions out of the second storage device 82.The mixture of parent ions having different m/z ratios represents amixture of different analyzed species. Ions are separated in time in thefirst analyzer 31 with an extended multiple folded ion path, exceeding30 m. The analyzer operates at reduced ion energy about 50 to 100 eV toextend separation time to about 10 ms. The MR-TOF of the presentinvention is very well suited for ion separation at reduced energies andprolonged flight times. The analyzer tolerates high relative energyspread (up to 20%) by providing a high order time-of-flight focusingwith respect to ion energy. It also provides an exceptional transmissionat reduced ion energies. Ions are bounced in X direction andperiodically focused in Z direction by ion mirrors. Simultaneously ionsare retained along the jig-saw folded trajectory because of periodicfocusing in a set of periodic lenses 17, thus providing periodicfocusing in X direction. The ion flight path is extended by reflectionsin the edge deflector 33. Initially injected ions follow path 35. Aftersteering in the edge deflector 32, ions follow trajectory 36 andexperience multiple bounces between mirrors. The trajectory 36approaches the second edge deflector 33 from the right. The edgedeflector 33 steers ions such that they follow trajectory 37. Suchsteering reverts the direction of ion drift along Y-axis. The trajectory37 again passes through multiple lenses and approaches to the edgedeflector 32 from the left. The static edge deflector 32 steers the beaminto the fragmentation cell 152. Note, that ion edge reflection is madeusing constant voltages. The flight path is doubled while retaining fullmass range of the analyzer.

The deflectors could be used in a pulsed mode for several purposes:

-   -   1. To further extend flight path at the expense of the mass        range. By pulse adjusting deflector 32 to a double deflecting        voltage the trajectory becomes enclosed. Ion coming along        trajectory 37 will be returned back into trajectory 36 and will        experience multiple edge deflections until deflector 32 is        switched back to a smaller deflection and ions are released        along the trajectory 39 or trajectory 38 in case deflector 32 is        switched off    -   2. To divert ions onto the off-line detector 34 after a single        edge deflection. The deflector 32 is switched off after heaviest        ions of trajectory 35 pass through the deflector into MR-TOF and        before lightest ions of trajectory 37 approach the deflector 32.    -   3. To bypass analyzer by steering the beam into the off-line        detector 34    -   4. To make a crude mass separation or suppression of unwanted        species, like low mass or very intense ions.

Parent ions are introduced into fragmentation cell 152 at a kineticenergy (about 50 to 100 eV) sufficiently high for ion decomposition. Asdescribed in a co-pending invention the fragmentation cell is filledwith gas, preferably at an elevated gas pressure above 0.1 Torr and thecell is kept short (about 1 cm). A higher (than usual 0.005 to 0.01Torr) gas pressure in the cell requires an additional envelope ofdifferential pumping with additional means of ion focusing eitherelectrostatic lenses or an RF focusing devices. Ion transfer through thecell is accelerated by axial DC field or a moving-wave axial field. As aresult ions pass the cell in about 20 us time, while spreading ionpacket by less than 10 us. The same field allows periodic storing andpulse ejection of ions, or at least a substantial synchronous modulationof ion velocities.

Fragment ions are then ejected out of the cell and into the second TOFanalyzer 161 for mass analysis. To improve efficiency of the secondanalyzer, ions are periodically bunched at about every 10 us at the exitof fragmentation cell 152 and those pulses are synchronized with pulsesof the orthogonal acceleration 163 in o-TOF 161. The second analyzer 161is adjusted to have a short flight time (10 to 30 us), which is expectedto be achieved at a moderate flight path (less than 1 m) and high ionenergies (above 5 kV). Drastically different time scales of twoanalyzers (at least 2 orders of magnitude) allow parallel MS-MS analysisof all parent ions. Fragments of different parent species are formed ata different time and a so-called time-nested data acquisition system isused to record separate fragment mass spectra without mixing themtogether.

Note, that in general the fragmentation cell may incorporate any RFstoring device described in the art or in the present invention. Byusing storing and periodic pulse ejection of the cell one may equallywell employ any other type of TOF MS, as long as it has short separationtime, around 10 us. For example, another MR-TOF MS may be used as asecond TOF analyzer, particularly if acceleration voltage is raisedhigher (say 5 kV) and flight path is adjusted short by using shift ionreflection.

The described MS-MS instrument is expected to have an extremely highthroughput of MS-MS analysis (up to hundreds MS-MS spectra a second),particularly valuable in combination with on-line separation techniques.Such tandems are expected to be applied for analysis of extremelycomplex mixtures, like combinatorial libraries in pharmaceutical studiesor peptide mixtures in proteome studies. The instrument has a limitedmass resolving power (resolution) of both stages of mass analysis.Assuming 1 ns time resolution of TOF2 data system and 10 ms separationtime in TOF1, the product of two mass resolving powers R1*R2 is lessthan 2.5*106, e.g. still making a powerful analytical combination ofR1=300-500 and R2-3000-5000, considering capabilities of parallel MS-MSanalysis. Note, that R1>300 is sufficient for separating between groupsof isotopes of parent ions and R2>3000 is sufficient for charge statedetermination of moderate mass ions (m/z<2000 a.m.u.).

Resolution of both stages may be improved by using a larger separationtime in TOF1. Stable retaining of ion beam in TOF1 would allow a muchlonger separation without losses in TOF1. Vacuum better than 10-11 Torrhas been achieved in FTMS, allowing extension of flight time to minutes.However, a possibility of further extension of TOF1 separation time muchbeyond 10 ms is somehow limited by space charge effects in the pulsingion trap. Space charge limit and limited storage time would not allowmuch higher resolution in both stages. As an example, combination ofR1=100,000 and R2=100,000 with a product R1*R2=1010 would require 40seconds storage time, requiring to store about 1010 ions generated byESI source at such period. An ion cloud of 1 mm diameter would havespace charge potential about 10 kV, impossible to trap. There arenumerous ways of reaching a compromise by limiting number of ions in thetrap below 106, either by limiting and controlling an ion injection timeinto a pulsing trap or by using a prior mass separation or by selectivefiltering out of abundant ion species. Such ion preparation steps couldbe made either in the intermediate ion guide 71 or in the second storagedevice 81.

Higher resolution of both MS stages seems to be incompatible withparallel analysis, since it requires ion losses by either attenuation ofthe entire beam (by limiting of injection time), or by separation ofdesired species or by filtering out of abundant species. However, itlooks more promising to combine rapid screening at low resolution withsubsequent data mining using a very high resolution in both stages.First step allows determining masses of parent ions of interest, whilesecond analysis step is used for high precision and confident analysisof those species.

FIG. 16, shows a preferred embodiment of a high resolution tandemtime-of-flight tandem mass spectrometer 171. The tandem 171 is similarto the above described tandem TOF-TOF 151, except of using timed ionselection in the first MR-TOF and using a second multi-reflectinganalyzer 31B for fragment analysis. The second MR-TOF analyzer 31B issomewhat similar to the first MR-TOF. It comprises a field-free region14B, two of planar gridless mirrors 15B, a set of periodic lenses 17B, adetector 34B and a pair of edge deflectors 32B and 33B. The secondanalyzer 31B also comprises an additional lens deflector 173incorporated into the second lens of periodic lens set 17B for thepurpose of flight path adjustment. Other elements of the tandem MS 171are similar to earlier described elements. The pulsed ion source 51comprises a continuous ion source, a dual storing ion guide and anaccelerator. The above described first MR-TOF MS 31A comprises afield-free region 14A, two of planar gridless mirrors ISA, a set ofperiodic lenses 17A, a pair of edge deflectors 32A and 33A, an off-linedetector 34A and also a timed ion selector 172 (not used in the secondMR-TOF 31B). The earlier described fast fragmentation cell 152 comprisesa short (5-30 mm) RF quadrupole 158, filled with gas at a relativelyhigh gas pressure (0.1-1 Torr) via port 157. The quadrupole issurrounded by inner cell 156 with focusing lenses 154 on both ends. Thecell preferably has means 159 and 160 for slowing and accelerating ofion passage through the cell, for example, by modulating axial DC field.

In operation, ions are stored in the pulsed ion source 51 and areejected into the first MR-TOF analyzer 31A for time-of-flightseparation. Separated ions or a portion of those ions are admitted bythe timed ion gate 172 into the fragmentation cell 152, where ionsundergo fragmentation. Periodically fragment ions are pulsed out of thecell 152 into the second MR-TOF analyzer 31B for mass analysis. Beloware described two modes of operation of the tandem—a high throughputmode of parallel MS-MS analysis and a high-resolution mode of sequentialMS-MS analysis.

In the first high throughput mode, the first analyzer is operated at areduced ion energy controlled by potential of floatable field freeregion 14A, adjusted to about −50 V. Separation takes about 10 ms timeand all parent ions are admitted into fragmentation cell 152. The timedion gate 172 remains off while admitting parent ions, though could beused for suppression of low mass range containing majority of solventions and chemical background ions. The second analyzer is adjusted to ahigh ion energy, controlled by potential of the field free region 14Bbeing held at about −5 kV, i.e. ion velocities are higher by one orderof magnitude compared to the first analyzer. The flight path in thesecond analyzer is substantially reduced by using an additionaldeflector 173, reverting ion drift direction. Ions experience only tworeflections in ion mirrors 15B and are directed into the detector 34B.Typical flight path of fragment ions becomes approximately 0.5 m i.e.almost 2 orders of magnitude shorter compared to the first MR-TOF 31A.Time scales are different by almost 3 orders of magnitude, which allowan earlier described parallel MS-MS analysis of multiple parent ionswith a time-nested data acquisition. Such analysis allows rapidallocation of parent ions having a range of desired fragments (forexample, for peptides composed of amino acids it is determined by thepresence of the so-called immonium ions). The information on parent ionmasses could be used for accelerating of detailed MS-MS analysis in thesecond analysis mode with a higher resolution and higher specificity.

In the second high resolution mode, both MR-TOF analyzers are operatedat an elevated energy and resolution. The energy is adjusted by applyingnegative high voltage potential (say −5 kV) to both field free regions14A and 14B. At typical flight path of 30 m, flight time appears around1 ms. As a result, the frequency of a pulsed ion source needs to beadjusted to 1 kHz. Extraction pulses in the second storage device areadjusted to provide for much higher strength of electric field, similarto those employed in a high resolution MR-TOF MS. A higher voltage (say−5 kV) pulses are applied to exit aperture 92 with correspondingpositive high voltage pulses (+5 kV) being applied to auxiliaryelectrodes 84. Higher strength of electric field causes proportionalreduction of turn around time (to 5 to 10 ns) and proportionalenlargement of ion energy spread (100-200 eV), estimated in case of 0.5mm size of ion cloud. Expected resolution of first MR-TOF analyzer isexpected to be in the order of 50,000 to 100,000.

To select a single species of ions at such resolution one would need 0.3mm spatial resolution of timed ion selector, reachable withBradbery-Nielsen gate—a device composed of two alternated rows of wires,located in one plane. By applying a short 10-30 ns pulse between tworows a short pulse of ions is admitted through the gate, while otherspecies are steered and would be lost at a subsequent stop. As anexample, timed ion gate is located near the first lens and in the planeof intermediate time-of-flight focusing. A 1000 V pulse applied to wiressteers 10 kV ions by 3 degrees (1/20), which is sufficient to miss 1 mmentrance aperture 153 of the CID cell. The resolution of parent ionselection may be further improved by using multiple edge reflectionswith simultaneous extension of the flight path and flight time in thefirst MR-TOF. The associated shrinking of mass range is no longerimportant, since the gate admits one m/z of parent ions anyway. In thiscase it is also desirable to reduce the energy spread of parent ionsbelow 50 eV at the cost of a larger turn-around time, which may becompensated by a longer flight path, lower acceleration energy andlonger flight time in the first analyzer.

Mass selected parent ions are decelerated to about 50-100 eV and arefocused at the entrance aperture of the fragmentation cell 152.Injection at such energies causes fragmentation of selected parent ions.Fragments are stored in the fragmentation cell 152 by RF confinement inRF trap 157 and by arranging axial DC well, formed by DC potentials ofauxiliary electrodes and of the exit aperture. By applying electricpulses to those electrodes, the fragment ions are pulse ejected into thesecond MR-TOF for mass analysis. Parameters of ion pulse and of thesecond analyzer are similar to those in the first MR-TOF. The CID cellmay incorporate various elements and schemes of pulsed ion sourcesdescribed earlier. Thus, mass analysis of fragments is expected at ahigh resolving power (resolution) about 50,000 to 100,000. The describedtandem allows a complete usage of analysis time. While fragment cell 152is emptied and fragment ions are mass separated in the second MR-TOF 31Bthe first analyzer 31A may be used for simultaneous selection of parentions and injection into the fragmentation cell.

FIG. 17 shows an economy tandem instrument 181 comprising a pulsed ionsource 51, a single MR-TOF analyzer 31 and an optional fragmentationcell 182. Either gas filled storage device of the tandem 181, includingstorage device 73 or 83 of the pulsed ion source 51 or the optionalfragmentation cell 182 can be used to fragment ions and to inject themback into the same MR-TOF for subsequent mass analysis or separation. Asa result, the instrument allows a high resolution sequential MS-MSanalysis or a multi-step MS^(n) sequential analysis, simply by repeatingsteps of ions selection, fragmentation and reverse injection.

Multiple usage of MR-TOF also requires minor adjustment of deflectionregimes in the MR-TOF. Let us consider an example of tandem 181 whichemploys the cell 182 for ion fragmentation. At a stage of parentseparation, both deflectors 32 and 33 stay on at constant steeringpotentials. Ions follow the sequence of trajectories 35, 36, 37 and 39.Timed ion gate 172 admits ions of interest into the cell along thetrajectory 39. Ions are decelerated to about 50-100 eV and undergofragmentation. Fragments are stored by RF fields on electrodes 187 andDC trapping potential formed by entrance aperture 184, auxiliaryelectrodes 188 and the back electrode 189. After sufficientpredetermined delay ions are collisional dampened and are pulse ejectedout of the cell towards the MR-TOF. They follow the revert trajectory39, then 37. However, at about the time of ion ejection from the cellthe deflector 33 is switched into a different deflecting mode. Ions aresteered at half angle, bounce from the right mirror along the trajectory190 and revert their motion along trajectory 37 and then 39. Then eitherdeflector 32 is turned off to pass all the ions onto the off-linedetector 34 or timed ion selector 172 is used to select daughter ions ofinterest to pass them into fragmentation cell for further steps ofMS^(n) analysis. Similarly, if storage ion guide 73 or 83 is used forion fragmentation, the returning of ions into the storage device couldbe arranged by deflector 33, deflecting ions at half angle. Afterstraight reflection in the mirror ions would return along the sametrajectory 36. This allows passing ions between fragmentation cell andMR-TOF analyzer for a desired number of cycles. Again, multiple edgedeflections could be used to enhance selection of single specimen. Adual storage arrangement also allows saving on ion duty cycle by storingcontinuously coming ions in the first compartment, while using thesecond compartment for a pulse ejection of prestored ions and then forion fragmentation in a multi-stage MS-MS analysis.

The described preferred embodiment is meant to be an explanatoryexample, not intended to be limiting. Further, it may be apparent tothose skillful of the art that numerous changes could be made whilestaying within the spirit and principle of the invention.

1. A multi-reflecting time-of-flight mass spectrometer (MR-TOF MS)comprising: an ion source; an ion receiver downstream from said ionsource; at least one ion mirror assembly intermediate said ion sourceand said ion receiver and elongated in a shift direction for improvingsensitivity and resolution of the MR-TOF MS; a drift space intermediatesaid ion mirror assembly; and a lens assembly disposed within said driftspace along said at least one shift direction and with a period in saidshift direction corresponding to ion shift per integer number of ionreflections, said ion source, ion receiver, ion mirror assembly and saiddrift space arranged to provide a folded ion path between said ionsource and said ion receiver composed of at least one reflection by saidion mirror assembly for separating ions in time according to theirmass-to-charge ratio (m/z) so that a flight time of the ions issubstantially independent of ion energy.
 2. The MR-TOF MS as defined inclaim 1, further comprising: a timed ion selector including one of aBradbury-Nielsen ion gate, a parallel plate deflector, and a controlgrid within said ion receiver.
 3. The MR-TOF MS as defined in claim 1,wherein said ion source comprises one of an ion storage device and anion accelerator.
 4. The MR-TOF MS as defined in claim 1, wherein saidion source comprises a continuous ion source.
 5. The MR-TOF MS asdefined in claim 1, wherein said ion source comprises one of a SIMS, aMALDI, and an IR-MALDI.
 6. The MR-TOF MS as defined in claim 4, whereinsaid ion source comprises one of an ESI, an APCI, an APPI, an EI, a CI,a PI, an ICP, a gas-filled MALDI, an atmospheric MALDI, a gaseous ionreaction cell, a DC/field asymmetric ion mobility spectrometer, and afragmentation cell.
 7. The MR-TOF MS as defined in claim 1, wherein saidion receiver includes an ion detector having an extended dynamic range.8. The MR-TOF MS as defined in claim 1, wherein said ion receivercomprises a gas-filled cell selected from one of a fragmentation cell, amolecular reaction cell, an ion reaction cell, electron capturedissociation, ion capture dissociation, a soft deposition cell, and acell for surface ion dissociation.
 9. A multi-reflecting time-of-flightmass spectrometer (MR-TOF MS) comprising: an ion source; an ion receiverdownstream from said ion source; at least one ion mirror assemblyintermediate said ion source and said ion receiver and elongated in ashift direction for improving sensitivity and resolution of the MR-TOFMS; and a drift space intermediate said ion mirror assembly, said ionsource, ion receiver, ion mirror assembly and said drift space arrangedto provide a folded ion path between said ion source and said ionreceiver composed of at least one reflection by said ion mirror assemblyfor separating ions in time according to their mass-to-charge ratio(m/z) so that a flight time of the ions is substantially independent ofion energy, wherein said ion mirror assembly comprises a plurality ofelectrodes shaped and spaced relative to one another to provide aspatial ion focusing and time-of-flight focusing of ions substantiallyindependent of ion energy and on ion position in a plane transverse tosaid ion path.
 10. The MR-TOF MS as defined in claim 1, wherein said ionmirror assembly includes one of a parallel assembly of conductive squareframes, slotted plates, bars, and rods, each having an optional edgetermination.
 11. The MR-TOF MS as defined in claim 1, wherein at least aportion of said ion mirror assembly is operably connected to a pulsedvoltage supply for gating ions in or out of the MR-TOF MS.
 12. TheMR-TOF MS as defined in claim 1, wherein said ion mirror assemblycomprises at least two electrodes having voltages of opposite polaritiesrelative to the other to form an attractive lens.
 13. The MR-TOF MS asdefined inclaim 1, wherein said drift space comprises an ion deflectorconnected to one of a DC voltage supply and a pulsed voltage supply. 14.The MR-TOF MS as defined in claim 1, wherein said lens assembly includesat least two lenses elongated transversely to said ion path.
 15. TheMR-TOF MS as defined in claim 3, wherein said ion storage devicecomprises a gas-filled set of electrodes having a radio-frequency (RF)voltage applied to at least one of said electrodes.
 16. The MR-TOF MS asdefined in claim 3, wherein said ion storage device comprises aplurality of sets of electrodes having a radio frequency (RF) voltageapplied to at least one electrode in a first set of electrodes and apulse voltage applied to at least one electrode in a second set ofelectrodes.
 17. The MR-TOF MS as defined in claim 3, wherein said ionaccelerator comprises a pulsed orthogonal accelerator.
 18. The MR-TOF MSas defined in claim 3, wherein said ion accelerator comprises aplurality of electrodes, each having a slit along said shift directionof the MR-TOF MS.
 19. The MR-TOF MS as defined in claim 3, wherein saidion accelerator comprises one of a pulsed ion mirror assembly and apulsed portion of said ion mirror assembly.
 20. The MR-TOF MS as definedin claim 3, wherein said ion accelerator comprises one of an acceleratorwith pulsed voltages and an accelerator with static voltages.
 21. TheMR-TOF MS as defined in claim 4, wherein said continuous ion sourcecomprises an intermediate ion storage guide preceding said ion storagedevice and having a gas pressure greater than said ion storage device.22. The MR-TOF MS as defined in claim 4, wherein said continuous ionsource comprises at least two gas-filled sets of electrodes having aradio-frequency (RF) voltage applied to at least one set of saidgas-filled electrodes.
 23. The MR-TOF MS as defined in claim 7, whereinsaid ion detector comprises one of a secondary electron multiplierhaving at least one dynode, a scintillator and photomultiplier, amicro-channel, micro-sphere plates, at least two channels of detection,and at least two anodes each connected to a data acquisition systemhaving an analog-to-digital converter (ADC).
 24. The MR-TOF MS asdefined in claim 7, wherein said ion detector dynamic range is extendedby alternating scans with various intensities of said pulsed ion source.25. The MR-TOF MS as defined in claim 7, wherein said ion detectordynamic range is extended by alternating scans with varying durations ofion injection into an ion storage device.
 26. The MR-TOF MS as definedin claim 8, wherein said gas-filled cell includes at least one electrodeconnected to a radio-frequency (RF) voltage for one of dampening ionkinetic energy in gas collisions, stabilizing internal ion energy,confining ions, fragmenting ions, selecting ion species and retainingions for exposure to reactant particles.
 27. The MR-TOF MS as defined inclaim 13, wherein said ion deflector comprises at least one steeringplate.
 28. The MR-TOF MS as defined in claim 13, wherein said iondeflector is located on a far side of said shift axis opposite to saidion source for steering ions in a static mode to change direction ofsaid ion path.
 29. The MR-TOF MS as defined in claim 13, wherein saidion deflector is located on a similar side of said shift axis as saidion source for directing ions toward one of an off-axis detector and anMR-TOF MS analyzer, and revert in a direction of ion shift for a time ofion confinement within the MR-TOF MS.
 30. The MR-TOF MS as defined inclaim 15, wherein said gas-filled set of electrodes comprises at leastone of an ion guide having a plurality of elongated rods, a 3-Dquadrapole ion trap, a linear ion trap with ion ejection, an RF channelwith at least one electrode having an opening for ion passage, a ringelectrode trap, a hybrid ion guide with a 3-D ion trap, and a segmentedanalog of the aforementioned electrodes formed of at least two plates.31. The MR-TOF MS as defined in claim 4, wherein said ion storage deviceincludes one of a filter of ion components, a discriminator of ioncomponents, and a suppressor of ion components.
 32. A tandemtime-of-flight mass spectrometer apparatus, comprising: a pulsed ionsource; said MR-TOF MS of claim 1 provided to separate parent ions; afragmentation cell downstream of said MR-TOF MS for fragmenting theparent ions into daughter ions; and a mass spectrometer downstream ofsaid fragmentation cell for detecting said daughter ions; wherein saidat least one ion mirror assembly comprises two grid-less and parallelion mirrors separated by a drift space and substantially elongated inone shift-direction.
 33. The mass spectrometer apparatus as defined inclaim 32, further comprising an ion selector subsequent saidfragmentation cell.
 34. The mass spectrometer apparatus as defined inclaim 32, wherein said fragmentation cell comprises a gas-filled cellhaving a differential pumping stage and an ion focusing device.
 35. Themass spectrometer apparatus as defined in claim 32, wherein saidfragmentation cell comprises an internal gas pressure P associated witha cell length L (P*L) above 0.2 Torr*cm.
 36. The mass spectrometerapparatus as defined in claim 32, wherein said fragmentation cellcomprises a gas pressure P>0.5 Torr and L<1 cm.
 37. The massspectrometer apparatus as defined in claim 32, wherein saidfragmentation cell comprises a gas filled set of electrodes having aradio frequency (RF) voltage applied to at least one of said electrodesfor confining ions in radial direction.
 38. The mass spectrometerapparatus as defined in claim 32, wherein said fragmentation cellfurther comprises a set of electrodes connected to one of a DC andslow-varying voltage to form an axial DC electric field, and an axialmoving-wave electric field to control velocity of ion motion in saidfragmentation cell, said DC voltage being applied to one of the same setof electrodes and a dissimilar set of electrodes.
 39. The massspectrometer apparatus as defined in claim 32, wherein said massspectrometer downstream of said fragmentation cell comprises atime-of-flight mass spectrometer (TOF MS).
 40. The mass spectrometerapparatus as defined in claim 39, wherein said TOF MS comprises anorthogonal ion accelerator.
 41. The mass spectrometer apparatus asdefined in claim 39, wherein said TOF MS comprises ion path less than,and an acceleration voltage greater than in said MR-TOF MS to produce anion flight time in said TOF MS at least 100-fold less than in saidMR-TOF MS.
 42. The mass spectrometer apparatus as defined in claim 39,wherein said TOF MS comprises a data system adapted for parallelacquisition of daughter spectra without mixing spectra corresponding todifferent parent ions.
 43. The mass spectrometer apparatus as defined inclaim 39, wherein said TOF MS includes a first and a secondmulti-reflecting time-of-flight mass spectrometer (MR-TOF MS).
 44. Themass spectrometer apparatus as defined in claim 43, wherein said secondMR-TOF MS is substantially identical in construction to said firstMR-TOF MS.
 45. The mass spectrometer apparatus as defined in claim 40,wherein said orthogonal ion accelerator is grid-less.
 46. The massspectrometer apparatus as defined in claim 44, wherein the second MR-TOFMS forming said TOF MS comprises a plurality of deflectors cooperatingwith lenses in said drift space to adjust a flight path of the ions insaid TOF MS.
 47. A tandem multi-reflecting time-of-flight massspectrometer (MR-TOF MS-MS) apparatus comprising: a firstmulti-reflecting time-of-flight mass spectrometer (MR-TOF MS) forseparating parent ions; a fragmentation cell attached to said firstMR-TOF MS for receiving said parent ions; and a second MR-TOF MSattached to said fragmentation cell for mass analysis of daughter ionsexiting said fragmentation cell, wherein at least one of said MR-TOF MScomprises at least two grid-less and parallel ion mirrors separated bydrift space and substantially elongated in one shift-direction, whereinat least one of said first and second MR-TOF MS comprises: an ionsource; an ion receiver downstream from said ion source; at least oneion mirror assembly intermediate said ion source and said ion receiverand elongated in a shift direction for improving sensitivity andresolution of the MR-TOF MS; a drift space intermediate said ion mirrorassembly; and a lens assembly disposed within said drift space alongsaid at least one shift direction and with a period in said shiftdirection corresponding to ion shift per integer number of ionreflections, said ion source, ion receiver, ion mirror assembly and saiddrift space arranged to provide a folded ion path between said ionsource and said ion receiver composed of at least one reflection by saidion mirror assembly for separating ions in time according to theirmass-to-charge ratio (m/z) so that a flight time of the ions issubstantially independent of ion energy.
 48. The tandem MR-TOF MS-MSapparatus as defined in claim 47, further comprising a timed ionselector between said first MR-TOF MS and said fragmentation cell. 49.The tandem MR-TOF MS-MS apparatus as defined in claim 47, wherein saidfragmentation cell further comprises at least one set of electrodesconnected to one of DC and slow varying voltage to form one of arespective axial DC electric field or an axial moving-wave electricfield, controlling velocity of ion motion within said fragmentationcell, and said DC voltage being applied to at least one electrode insaid at least one set as RF voltage.
 50. The tandem MR-TOF MS-MSapparatus as defined in claim 47, wherein said fragmentation cellfurther includes a gas at a gas pressure (P) above P*L>0.2 Torr*cm. 51.The tandem MR-TOF MS-MS apparatus as defined in claim 47, wherein saidfragmentation cell comprises a differential pumping stage and an ionfocusing assembly.
 52. The tandem MR-TOF MS-MS apparatus as defined inclaim 47, wherein said fragmentation cell comprises at least onegas-filled set of electrodes having a radio frequency (RF) voltageapplied to at least one electrode within said set of electrodes toconfine ions in a radial direction.
 53. The tandem MR-TOF MS-MSapparatus as defined in claim 47, wherein said fragmentation cellcomprises means for ion storage and pulsed ejection in one of an axialand an orthogonal direction.
 54. The tandem MR-TOF MS-MS apparatus asdefined in claim 50, wherein said second TOF MS comprises an orthogonalion accelerator.
 55. The tandem MR-TOF MS-MS apparatus as defined inclaim 53, wherein said second MR-TOF MS comprises means for adjusting anion path less than, and an acceleration voltage greater than, said firstMR-TOF MS such that a flight time in said TOF MS is at least 100-foldless compared to said flight time in said first MR-TOF MS.
 56. Thetandem MR-TOF MS-MS apparatus as defined in claim 52, wherein saidsecond MR-TOF MS comprises a data system providing parallel acquisitionof daughter spectra without mixing spectra from unrelated parent ions.57. The tandem MR-TOF MS-MS apparatus as defined in claim 56, whereinsaid second MR-TOF MS comprises a lens assembly disposed within saiddrift space.
 58. The tandem MR-TOF MS-MS apparatus as defined in claim57, wherein said lens assembly comprises at least one deflectorconfigured to adjust a flight path of ions in said second MR-TOF MS. 59.A multi-reflecting time-of-flight mass spectrometer (MR-TOF MS-MS)apparatus comprising: a multi-reflecting time-of-flight massspectrometer (MR-TOF MS); and a fragmentation cell connected to saidMR-TOF MS and configured to revert ions within said MR-TOF MS to employthe same MR-TOF analyzer for analysis of both parent ions and fragmentions, wherein said MR-TOF MS comprises an assembly of two grid-less andparallel ion mirrors separated by drift space and substantiallyelongated in one shift-direction, wherein said MR-TOF MS comprises: anion source; an ion receiver downstream from said ion source; at leastone ion mirror assembly intermediate said ion source and said ionreceiver and elongated in a shift direction for improving sensitivityand resolution of the MR-TOF MS; a drift space intermediate said ionmirror assembly; and a lens assembly disposed within said drift spacealong said at least one shift direction and with a period in said shiftdirection corresponding to ion shift per integer number of ionreflections, said ion source, ion receiver, ion mirror assembly and saiddrift space arranged to provide a folded ion-path between said ionsource and said ion receiver composed of at least one reflection by saidion mirror assembly for separating ions in time according to theirmass-to-charge ratio (m/z) so that a flight time of the ions issubstantially independent of ion energy.